diff options
72 files changed, 1131 insertions, 1108 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index dd6db7d6..5f4e0f9a 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -60,7 +60,7 @@ GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) echo GN2_BASE_DIR=$GN2_BASE_DIR -GUIX_SITE=$GN2_BASE_DIR/lib/python2.7/site-packages +GUIX_SITE=$GN2_BASE_DIR/lib/python3.8/site-packages if [ -d $GUIX_SITE ]; then echo INFO: GN2 is running from GNU Guix GN2_BASE_DIR=$GUIX_SITE @@ -105,7 +105,7 @@ echo GN2_SETTINGS=$settings # if [ -z $ELASTICSEARCH_PROFILE ]; then # echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE"; # else -# PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" +# PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python3.8/site-packages" # fi if [ -z $GN2_PROFILE ] ; then @@ -121,7 +121,7 @@ if [ -z $GN2_PROFILE ]; then read -p "PRESS [ENTER] TO CONTINUE..." else export PATH=$GN2_PROFILE/bin:$PATH - export PYTHONPATH="$PYTHON_GN_PATH:$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!! + export PYTHONPATH="$GN2_PROFILE/lib/python3.8/site-packages" # never inject another PYTHONPATH!! export R_LIBS_SITE=$GN2_PROFILE/site-library export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index 19e4d14f..fffa9571 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -167,7 +167,7 @@ the Guix suggested environment vars. Check the output of #+begin_src bash guix package --search-paths -export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages" +export PYTHONPATH="/root/.guix-profile/lib/python3.8/site-packages" export R_LIBS_SITE="/root/.guix-profile/site-library/" #+end_src @@ -265,7 +265,7 @@ software. If something is not working, take a hint from the settings file that comes in the Guix installation. It sits in something like -: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py +: cat ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py ** Set up nginx port forwarding @@ -380,7 +380,7 @@ After setting the paths for the server #+begin_src bash export PATH=~/.guix-profile/bin:$PATH -export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" +export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages" export R_LIBS_SITE="$HOME/.guix-profile/site-library/" export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0" export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0" diff --git a/doc/README.org b/doc/README.org index 46df03c7..43c92e3c 100644 --- a/doc/README.org +++ b/doc/README.org @@ -218,7 +218,7 @@ information given by guix: On one system: -: export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" +: export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages" : export R_LIBS_SITE="$HOME/.guix-profile/site-library/" : export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0" diff --git a/doc/development.org b/doc/development.org index e65ccd58..cd3beea3 100644 --- a/doc/development.org +++ b/doc/development.org @@ -67,11 +67,11 @@ You can install a Python package locally with pip, e.g. pip install hjson #+END_SRC -This installed in ~$HOME/.local/lib/python2.7/site-packages~. To add +This installed in ~$HOME/.local/lib/python3.8/site-packages~. To add the search path for GeneNetwork use the environment variable #+BEGIN_SRC sh -export PYTHON_GN_PATH=$HOME/.local/lib/python2.7/site-packages +export PYTHON_GN_PATH=$HOME/.local/lib/python3.8/site-packages #+END_SRC Now you should be able to do diff --git a/etc/default_settings.py b/etc/default_settings.py index f368237b..27522187 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -19,12 +19,12 @@ # # For GNU Guix deployment also check the paths in # -# ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py +# ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py import os import sys -GN_VERSION = open("../etc/VERSION","r").read() +GN_VERSION = open("../etc/VERSION", "r").read() GN_SERVER_URL = "http://localhost:8880/" # REST API server # ---- MySQL diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py index e50dbd40..35f2d1a1 100755 --- a/scripts/maintenance/QTL_Reaper_v6.py +++ b/scripts/maintenance/QTL_Reaper_v6.py @@ -7,7 +7,7 @@ import reaper import MySQLdb import time -con = MySQLdb.Connect(db='db_webqtl',user='username',passwd='', host="localhost") +con = MySQLdb.Connect(db='db_webqtl', user='username', passwd='', host="localhost") cursor = con.cursor() genotypeDir = '/gnshare/gn/web/genotypes/' @@ -23,7 +23,7 @@ for item in results: ProbeSetFreezeIds=sys.argv[1:] if ProbeSetFreezeIds: #####convert the Ids to integer - ProbeSetFreezeIds=map(int, ProbeSetFreezeIds) + ProbeSetFreezeIds=list(map(int, ProbeSetFreezeIds)) else: #####get all of the dataset that need be updated @@ -53,7 +53,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds: #if InbredSetId==12: # InbredSetId=2 - print ProbeSetFreezeId, InbredSets[InbredSetId] + print((ProbeSetFreezeId, InbredSets[InbredSetId])) genotype_1.read(InbredSets[InbredSetId]) locuses = [] @@ -102,7 +102,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds: kj += 1 if kj%1000==0: - print ProbeSetFreezeId, InbredSets[InbredSetId],kj + print((ProbeSetFreezeId, InbredSets[InbredSetId], kj)) - print ProbeSetFreezeIds + print(ProbeSetFreezeIds) diff --git a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py index 0f8602c9..bf796df4 100644 --- a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py +++ b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py @@ -24,4 +24,4 @@ for row in csv_data: #close the connection to the database. mydb.commit() cursor.close() -print "Done" \ No newline at end of file +print("Done") \ No newline at end of file diff --git a/scripts/maintenance/delete_genotypes.py b/scripts/maintenance/delete_genotypes.py index fa693f0f..b7f83758 100755 --- a/scripts/maintenance/delete_genotypes.py +++ b/scripts/maintenance/delete_genotypes.py @@ -8,26 +8,26 @@ import genotypes def main(argv): # config config = utilities.get_config(argv[1]) - print "config:" + print("config:") for item in config.items('config'): - print "\t%s" % (str(item)) + print(("\t%s" % (str(item)))) # var - print "variable:" + print("variable:") inbredsetid = config.get('config', 'inbredsetid') - print "\tinbredsetid: %s" % inbredsetid + print(("\tinbredsetid: %s" % inbredsetid)) # datafile datafile = open(config.get('config', 'datafile'), 'r') datafile = csv.reader(datafile, delimiter='\t', quotechar='"') - datafile.next() + next(datafile) delrowcount = 0 for row in datafile: if len(row) == 0: continue genoname = row[0] delrowcount += genotypes.delete(genoname, inbredsetid) - print "deleted %d genotypes" % (delrowcount) + print(("deleted %d genotypes" % (delrowcount))) if __name__ == "__main__": - print "command line arguments:\n\t%s" % sys.argv + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) - print "exit successfully" + print("exit successfully") diff --git a/scripts/maintenance/delete_phenotypes.py b/scripts/maintenance/delete_phenotypes.py index 326c466e..60dbec61 100755 --- a/scripts/maintenance/delete_phenotypes.py +++ b/scripts/maintenance/delete_phenotypes.py @@ -8,13 +8,13 @@ import phenotypes def main(argv): # config config = utilities.get_config(argv[1]) - print "config:" + print("config:") for item in config.items('config'): - print "\t%s" % (str(item)) + print(("\t%s" % (str(item)))) # var - print "variable:" + print("variable:") inbredsetid = config.get('config', 'inbredsetid') - print "\tinbredsetid: %s" % inbredsetid + print(("\tinbredsetid: %s" % inbredsetid)) # datafile datafile = open(config.get('config', 'datafile'), 'r') datafile = csv.reader(datafile, delimiter='\t', quotechar='"') @@ -27,9 +27,9 @@ def main(argv): except: continue delrowcount += phenotypes.delete(publishxrefid=publishxrefid, inbredsetid=inbredsetid) - print "deleted %d phenotypes" % (delrowcount) + print(("deleted %d phenotypes" % (delrowcount))) if __name__ == "__main__": - print "command line arguments:\n\t%s" % sys.argv + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) - print "exit successfully" + print("exit successfully") diff --git a/scripts/maintenance/load_genotypes.py b/scripts/maintenance/load_genotypes.py index 338483f4..51278d48 100755 --- a/scripts/maintenance/load_genotypes.py +++ b/scripts/maintenance/load_genotypes.py @@ -8,7 +8,7 @@ def main(argv): config = utilities.get_config(argv[1]) print("config file:") for item in config.items('config'): - print("\t%s" % str(item)) + print(("\t%s" % str(item))) parse_genofile(config, fetch_parameters(config)) def fetch_parameters(config): @@ -19,8 +19,8 @@ def fetch_parameters(config): config_dic['dataid'] = datastructure.get_nextdataid_genotype() config_dic['genofile'] = config.get('config', 'genofile') print("config dictionary:") - for k, v in config_dic.items(): - print("\t%s: %s" % (k, v)) + for k, v in list(config_dic.items()): + print(("\t%s: %s" % (k, v))) return config_dic def parse_genofile(config, config_dic): @@ -42,10 +42,10 @@ def parse_genofile(config, config_dic): if line.lower().startswith("chr"): # print("geno file meta dictionary:") - for k, v in meta_dic.items(): - print("\t%s: %s" % (k, v)) + for k, v in list(meta_dic.items()): + print(("\t%s: %s" % (k, v))) # - print("geno file head:\n\t%s" % line) + print(("geno file head:\n\t%s" % line)) strainnames = line.split()[4:] config_dic['strains'] = datastructure.get_strains_bynames(inbredsetid=config_dic['inbredsetid'], strainnames=strainnames, updatestrainxref="yes") continue @@ -81,7 +81,7 @@ def check_or_insert_geno(config_dic, marker_dic): result = cursor.fetchone() if result: genoid = result[0] - print("get geno record: %d" % genoid) + print(("get geno record: %d" % genoid)) else: sql = """ INSERT INTO Geno @@ -95,7 +95,7 @@ def check_or_insert_geno(config_dic, marker_dic): cursor.execute(sql, (config_dic['speciesid'], marker_dic['locus'], marker_dic['locus'], marker_dic['chromosome'], marker_dic['mb'])) rowcount = cursor.rowcount genoid = con.insert_id() - print("INSERT INTO Geno: %d record: %d" % (rowcount, genoid)) + print(("INSERT INTO Geno: %d record: %d" % (rowcount, genoid))) return genoid def check_genoxref(config_dic, marker_dic): @@ -146,9 +146,9 @@ def insert_genoxref(config_dic, marker_dic): """ cursor.execute(sql, (config_dic['genofreezeid'], marker_dic['genoid'], config_dic['dataid'], marker_dic['cm'], 'N')) rowcount = cursor.rowcount - print("INSERT INTO GenoXRef: %d record" % (rowcount)) + print(("INSERT INTO GenoXRef: %d record" % (rowcount))) if __name__ == "__main__": - print("command line arguments:\n\t%s" % sys.argv) + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) print("exit successfully") diff --git a/scripts/maintenance/load_phenotypes.py b/scripts/maintenance/load_phenotypes.py index c3c6570b..759d2eec 100755 --- a/scripts/maintenance/load_phenotypes.py +++ b/scripts/maintenance/load_phenotypes.py @@ -7,37 +7,37 @@ import datastructure def main(argv): # config config = utilities.get_config(argv[1]) - print "config:" + print("config:") for item in config.items('config'): - print "\t%s" % (str(item)) + print(("\t%s" % (str(item)))) # var inbredsetid = config.get('config', 'inbredsetid') - print "inbredsetid: %s" % inbredsetid + print(("inbredsetid: %s" % inbredsetid)) species = datastructure.get_species(inbredsetid) speciesid = species[0] - print "speciesid: %s" % speciesid + print(("speciesid: %s" % speciesid)) dataid = datastructure.get_nextdataid_phenotype() - print "next data id: %s" % dataid + print(("next data id: %s" % dataid)) cursor, con = utilities.get_cursor() # datafile datafile = open(config.get('config', 'datafile'), 'r') phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"') - phenotypedata_head = phenotypedata.next() - print "phenotypedata head:\n\t%s" % phenotypedata_head + phenotypedata_head = next(phenotypedata) + print(("phenotypedata head:\n\t%s" % phenotypedata_head)) strainnames = phenotypedata_head[1:] strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes") # metafile metafile = open(config.get('config', 'metafile'), 'r') phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"') - phenotypemeta_head = phenotypemeta.next() - print "phenotypemeta head:\n\t%s" % phenotypemeta_head - print + phenotypemeta_head = next(phenotypemeta) + print(("phenotypemeta head:\n\t%s" % phenotypemeta_head)) + print() # load for metarow in phenotypemeta: # - datarow_value = phenotypedata.next() - datarow_se = phenotypedata.next() - datarow_n = phenotypedata.next() + datarow_value = next(phenotypedata) + datarow_se = next(phenotypedata) + datarow_n = next(phenotypedata) # Phenotype sql = """ INSERT INTO Phenotype @@ -67,7 +67,7 @@ def main(argv): )) rowcount = cursor.rowcount phenotypeid = con.insert_id() - print "INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid) + print(("INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid))) # Publication publicationid = None # reset pubmed_id = utilities.to_db_string(metarow[0], None) @@ -81,7 +81,7 @@ def main(argv): re = cursor.fetchone() if re: publicationid = re[0] - print "get Publication record: %d" % publicationid + print(("get Publication record: %d" % publicationid)) if not publicationid: sql = """ INSERT INTO Publication @@ -109,7 +109,7 @@ def main(argv): )) rowcount = cursor.rowcount publicationid = con.insert_id() - print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid) + print(("INSERT INTO Publication: %d record: %d" % (rowcount, publicationid))) # data for index, strain in enumerate(strains): # @@ -158,14 +158,14 @@ def main(argv): cursor.execute(sql, (inbredsetid, phenotypeid, publicationid, dataid, "")) rowcount = cursor.rowcount publishxrefid = con.insert_id() - print "INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid) + print(("INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid))) # for loop next dataid += 1 - print + print() # release con.close() if __name__ == "__main__": - print "command line arguments:\n\t%s" % sys.argv + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) - print "exit successfully" + print("exit successfully") diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py index e9c8f25c..59a51cf9 100755 --- a/scripts/maintenance/readProbeSetMean_v7.py +++ b/scripts/maintenance/readProbeSetMean_v7.py @@ -31,20 +31,20 @@ def translateAlias(str): dataStart = 1 -GeneChipId = int( raw_input("Enter GeneChipId:") ) -ProbeSetFreezeId = int( raw_input("Enter ProbeSetFreezeId:") ) -input_file_name = raw_input("Enter file name with suffix:") +GeneChipId = int( input("Enter GeneChipId:") ) +ProbeSetFreezeId = int( input("Enter ProbeSetFreezeId:") ) +input_file_name = input("Enter file name with suffix:") fp = open("%s" % input_file_name, 'rb') try: passwd = getpass.getpass('Please enter mysql password here : ') - con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd) + con = MySQLdb.Connect(db='db_webqtl', host='localhost', user='username', passwd=passwd) db = con.cursor() - print "You have successfully connected to mysql.\n" + print("You have successfully connected to mysql.\n") except: - print "You entered incorrect password.\n" + print("You entered incorrect password.\n") sys.exit(0) time0 = time.time() @@ -55,22 +55,22 @@ time0 = time.time() # generate the gene list of expression data here # ######################################################################### -print 'Checking if each line have same number of members' +print('Checking if each line have same number of members') GeneList = [] isCont = 1 header = fp.readline() -header = string.split(string.strip(header),'\t') -header = map(string.strip, header) +header = string.split(string.strip(header), '\t') +header = list(map(string.strip, header)) nfield = len(header) line = fp.readline() kj=0 while line: - line2 = string.split(string.strip(line),'\t') - line2 = map(string.strip, line2) + line2 = string.split(string.strip(line), '\t') + line2 = list(map(string.strip, line2)) if len(line2) != nfield: - print "Error : " + line + print(("Error : " + line)) isCont = 0 GeneList.append(line2[0]) @@ -78,30 +78,29 @@ while line: kj+=1 if kj%100000 == 0: - print 'checked ',kj,' lines' + print(('checked ', kj, ' lines')) -GeneList = map(string.lower, GeneList) -GeneList.sort() +GeneList = sorted(map(string.lower, GeneList)) if isCont==0: sys.exit(0) -print 'used ',time.time()-time0,' seconds' +print(('used ', time.time()-time0, ' seconds')) ######################################################################### # # Check if each strain exist in database # generate the string id list of expression data here # ######################################################################### -print 'Checking if each strain exist in database' +print('Checking if each strain exist in database') isCont = 1 fp.seek(0) header = fp.readline() -header = string.split(string.strip(header),'\t') -header = map(string.strip, header) -header = map(translateAlias, header) +header = string.split(string.strip(header), '\t') +header = list(map(string.strip, header)) +header = list(map(translateAlias, header)) header = header[dataStart:] Ids = [] for item in header: @@ -109,26 +108,26 @@ for item in header: db.execute('select Id from Strain where Name = "%s"' % item) Ids.append(db.fetchall()[0][0]) except: - print item,'does not exist, check the if the strain name is correct' + print((item, 'does not exist, check the if the strain name is correct')) isCont=0 if isCont==0: sys.exit(0) -print 'used ',time.time()-time0,' seconds' +print(('used ', time.time()-time0, ' seconds')) ######################################################################## # # Check if each ProbeSet exist in database # ######################################################################## -print 'Check if each ProbeSet exist in database' +print('Check if each ProbeSet exist in database') ##---- find PID is name or target ----## line = fp.readline() line = fp.readline() -line2 = string.split(string.strip(line),'\t') -line2 = map(string.strip, line2) +line2 = string.split(string.strip(line), '\t') +line2 = list(map(string.strip, line2)) PId = line2[0] db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % (PId, GeneChipId) ) @@ -146,11 +145,10 @@ Names = [] for item in results: Names.append(item[0]) -print Names +print(Names) -Names = map(string.lower, Names) +Names = sorted(map(string.lower, Names)) -Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --# ##---- compare genelist with names ----## @@ -170,7 +168,7 @@ while x<len(GeneList) and y<len(Names): y += 1 if x%100000==0: - print 'check Name, checked %d lines'%x + print(('check Name, checked %d lines'%x)) while x<len(GeneList): GeneList2.append(GeneList[x]) @@ -180,20 +178,20 @@ isCont=1 ferror = open("ProbeSetError.txt", "wb") for item in GeneList2: ferror.write(item + " doesn't exist \n") - print item, " doesn't exist, check if the ProbeSet name is correct" + print((item, " doesn't exist, check if the ProbeSet name is correct")) isCont = 0 if isCont==0: sys.exit(0) -print 'used ',time.time()-time0,' seconds' +print(('used ', time.time()-time0, ' seconds')) ######################################################################### # # Insert data into database # ######################################################################### -print 'getting ProbeSet/Id' +print('getting ProbeSet/Id') #---- get Name/Id map ----# @@ -202,16 +200,16 @@ results = db.fetchall() NameIds = {} for item in results: NameIds[item[0]] = item[1] -print 'used ',time.time()-time0,' seconds' +print(('used ', time.time()-time0, ' seconds')) -print 'inserting data' +print('inserting data') ##---- get old max dataId ----## db.execute('select max(Id) from ProbeSetData') maxDataId = int(db.fetchall()[0][0]) bmax = maxDataId -print "old_max = %d\n" % bmax +print(("old_max = %d\n" % bmax)) ##---- insert data ----## fp.seek(0) @@ -222,8 +220,8 @@ kj = 0 values1 = [] values2 = [] while line: - line2 = string.split(string.strip(line),'\t') - line2 = map(string.strip, line2) + line2 = string.split(string.strip(line), '\t') + line2 = list(map(string.strip, line2)) PId = line2[0] recordId = NameIds[PId] @@ -255,8 +253,8 @@ while line: values1=[] values2=[] - print 'Inserted ', kj,' lines' - print 'used ',time.time()-time0,' seconds' + print(('Inserted ', kj, ' lines')) + print(('used ', time.time()-time0, ' seconds')) line = fp.readline() diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index fd6f0bb8..20a846a4 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -1,254 +1,254 @@ -#!/usr/bin/python2 -"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value""" -######################################################################## -# Last Updated Sep 27, 2011 by Xiaodong -# This version fix the bug that incorrectly exclude the first 2 probesetIDs -######################################################################## - -import string -import sys -import MySQLdb -import getpass -import time - - -def translateAlias(str): - if str == "B6": - return "C57BL/6J" - elif str == "D2": - return "DBA/2J" - else: - return str - -######################################################################## -# -# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile -# -######################################################################## - -dataStart = 1 - -GeneChipId = int( raw_input("Enter GeneChipId:") ) -ProbeSetFreezeId = int( raw_input("Enter ProbeSetFreezeId:") ) -input_file_name = raw_input("Enter file name with suffix:") - -fp = open("%s" % input_file_name, 'rb') - - -try: - passwd = getpass.getpass('Please enter mysql password here : ') - con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd) - - db = con.cursor() - print "You have successfully connected to mysql.\n" -except: - print "You entered incorrect password.\n" - sys.exit(0) - -time0 = time.time() -######################################################################## -# -# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile -# -######################################################################## - -#GeneChipId = 4 -#dataStart = 1 -#ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP -#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb') - - -######################################################################### -# -# Check if each line have same number of members -# generate the gene list of expression data here -# -######################################################################### -print 'Checking if each line have same number of members' - -GeneList = [] -isCont = 1 -header = fp.readline() -header = string.split(string.strip(header),'\t') -header = map(string.strip, header) -nfield = len(header) -line = fp.readline() - -kj=0 -while line: - line2 = string.split(string.strip(line),'\t') - line2 = map(string.strip, line2) - if len(line2) != nfield: - print "Error : " + line - isCont = 0 - - GeneList.append(line2[0]) - line = fp.readline() - - kj+=1 - if kj%100000 == 0: - print 'checked ',kj,' lines' - -GeneList = map(string.lower, GeneList) -GeneList.sort() - -if isCont==0: - sys.exit(0) - - -print 'used ',time.time()-time0,' seconds' -######################################################################### -# -# Check if each strain exist in database -# generate the string id list of expression data here -# -######################################################################### -print 'Checking if each strain exist in database' - -isCont = 1 -fp.seek(0) -header = fp.readline() -header = string.split(string.strip(header),'\t') -header = map(string.strip, header) -header = map(translateAlias, header) -header = header[dataStart:] -Ids = [] -for item in header: - try: - db.execute('select Id from Strain where Name = "%s"' % item) - Ids.append(db.fetchall()[0][0]) - except: - print item,'does not exist, check the if the strain name is correct' - isCont=0 - -if isCont==0: - sys.exit(0) - - -print 'used ',time.time()-time0,' seconds' -######################################################################## -# -# Check if each ProbeSet exist in database -# -######################################################################## -print 'Check if each ProbeSet exist in database' - -##---- find PID is name or target ----## -line = fp.readline() -line = fp.readline() -line2 = string.split(string.strip(line),'\t') -line2 = map(string.strip, line2) -PId = line2[0] - -db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % (PId, GeneChipId)) -results = db.fetchall() -IdStr = 'TargetId' -if len(results)>0: - IdStr = 'Name' - - -##---- get Name/TargetId list from database ----## -db.execute('select distinct(%s) from ProbeSet where ChipId=%d order by %s' % (IdStr, GeneChipId, IdStr)) -results = db.fetchall() - -Names = [] -for item in results: - Names.append(item[0]) -Names = map(string.lower, Names) -Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --# - -##---- compare genelist with names ----## -x=y=0 -x1=-1 -GeneList2=[] -while x<len(GeneList) and y<len(Names): - if GeneList[x]==Names[y]: - x += 1 - y += 1 - elif GeneList[x]<Names[y]: - if x!=x1: - GeneList2.append(GeneList[x]) - x1 = x - x += 1 - elif GeneList[x]>Names[y]: - y += 1 - - if x%100000==0: - print 'check Name, checked %d lines'%x - -while x<len(GeneList): - GeneList2.append(GeneList[x]) - x += 1 - -isCont=1 -ferror = open("ProbeSetError.txt", "wb") -for item in GeneList2: - ferror.write(item + " doesn't exist \n") - print item, " doesn't exist" - isCont = 0 - -if isCont==0: - sys.exit(0) - - -print 'used ',time.time()-time0,' seconds' -############################# -#Insert new Data into SE -############################ -db.execute(""" - select ProbeSet.%s, ProbeSetXRef.DataId from ProbeSet, ProbeSetXRef - where ProbeSet.Id=ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId=%d""" - % (IdStr, ProbeSetFreezeId)) -results = db.fetchall() - -ProbeNameId = {} -for Name, Id in results: - ProbeNameId[Name] = Id - -ferror = open("ProbeError.txt", "wb") - -DataValues = [] - -fp.seek(0) #XZ add this line -line = fp.readline() #XZ add this line -line = fp.readline() - -kj = 0 -while line: - line2 = string.split(string.strip(line),'\t') - line2 = map(string.strip, line2) - - CellId = line2[0] - if not ProbeNameId.has_key(CellId): - ferror.write(CellId + " doesn't exist\n") - print CellId, " doesn't exist" - else: - DataId = ProbeNameId[CellId] - datasorig = line2[dataStart:] - - i = 0 - for item in datasorig: - if item != '': - value = '('+str(DataId)+','+str(Ids[i])+','+str(item)+')' - DataValues.append(value) - i += 1 - - kj += 1 - if kj % 100 == 0: - Dataitems = ','.join(DataValues) - cmd = 'insert ProbeSetSE values %s' % Dataitems - db.execute(cmd) - - DataValues = [] - print 'inserted ',kj,' lines' - print 'used ',time.time()-time0,' seconds' - line = fp.readline() - -if len(DataValues)>0: - DataValues = ','.join(DataValues) - cmd = 'insert ProbeSetSE values %s' % DataValues - db.execute(cmd) - -con.close() - - +#!/usr/bin/python2 +"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value""" +######################################################################## +# Last Updated Sep 27, 2011 by Xiaodong +# This version fix the bug that incorrectly exclude the first 2 probesetIDs +######################################################################## + +import string +import sys +import MySQLdb +import getpass +import time + + +def translateAlias(str): + if str == "B6": + return "C57BL/6J" + elif str == "D2": + return "DBA/2J" + else: + return str + +######################################################################## +# +# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile +# +######################################################################## + + +dataStart = 1 + +GeneChipId = int(input("Enter GeneChipId:")) +ProbeSetFreezeId = int(input("Enter ProbeSetFreezeId:")) +input_file_name = input("Enter file name with suffix:") + +fp = open("%s" % input_file_name, 'rb') + + +try: + passwd = getpass.getpass('Please enter mysql password here : ') + con = MySQLdb.Connect(db='db_webqtl', host='localhost', + user='username', passwd=passwd) + + db = con.cursor() + print("You have successfully connected to mysql.\n") +except: + print("You entered incorrect password.\n") + sys.exit(0) + +time0 = time.time() +######################################################################## +# +# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile +# +######################################################################## + +#GeneChipId = 4 +#dataStart = 1 +# ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP +#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb') + + +######################################################################### +# +# Check if each line have same number of members +# generate the gene list of expression data here +# +######################################################################### +print('Checking if each line have same number of members') + +GeneList = [] +isCont = 1 +header = fp.readline() +header = string.split(string.strip(header), '\t') +header = list(map(string.strip, header)) +nfield = len(header) +line = fp.readline() + +kj = 0 +while line: + line2 = string.split(string.strip(line), '\t') + line2 = list(map(string.strip, line2)) + if len(line2) != nfield: + isCont = 0 + print(("Error : " + line)) + + GeneList.append(line2[0]) + line = fp.readline() + + kj += 1 + if kj % 100000 == 0: + print(('checked ', kj, ' lines')) + +GeneList = sorted(map(string.lower, GeneList)) + +if isCont == 0: + sys.exit(0) + + +print(('used ', time.time()-time0, ' seconds')) +######################################################################### +# +# Check if each strain exist in database +# generate the string id list of expression data here +# +######################################################################### +print('Checking if each strain exist in database') + +isCont = 1 +fp.seek(0) +header = fp.readline() +header = string.split(string.strip(header), '\t') +header = list(map(string.strip, header)) +header = list(map(translateAlias, header)) +header = header[dataStart:] +Ids = [] +for item in header: + try: + db.execute('select Id from Strain where Name = "%s"' % item) + Ids.append(db.fetchall()[0][0]) + except: + isCont = 0 + print((item, 'does not exist, check the if the strain name is correct')) + +if isCont == 0: + sys.exit(0) + + +print(('used ', time.time()-time0, ' seconds')) +######################################################################## +# +# Check if each ProbeSet exist in database +# +######################################################################## +print('Check if each ProbeSet exist in database') + +##---- find PID is name or target ----## +line = fp.readline() +line = fp.readline() +line2 = string.split(string.strip(line), '\t') +line2 = list(map(string.strip, line2)) +PId = line2[0] + +db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % + (PId, GeneChipId)) +results = db.fetchall() +IdStr = 'TargetId' +if len(results) > 0: + IdStr = 'Name' + + +##---- get Name/TargetId list from database ----## +db.execute('select distinct(%s) from ProbeSet where ChipId=%d order by %s' % ( + IdStr, GeneChipId, IdStr)) +results = db.fetchall() + +Names = [] +for item in results: + Names.append(item[0]) + Names = sorted(map(string.lower, Names)) + +##---- compare genelist with names ----## +x = y = 0 +x1 = -1 +GeneList2 = [] +while x < len(GeneList) and y < len(Names): + if GeneList[x] == Names[y]: + x += 1 + y += 1 + elif GeneList[x] < Names[y]: + if x != x1: + GeneList2.append(GeneList[x]) + x1 = x + x += 1 + elif GeneList[x] > Names[y]: + y += 1 + + if x % 100000 == 0: + print(('check Name, checked %d lines' % x)) + +while x < len(GeneList): + GeneList2.append(GeneList[x]) + x += 1 + +isCont = 1 +ferror = open("ProbeSetError.txt", "wb") +for item in GeneList2: + ferror.write(item + " doesn't exist \n") + isCont = 0 + + print((item, " doesn't exist")) +if isCont == 0: + sys.exit(0) + + +print(('used ', time.time()-time0, ' seconds')) +############################# +# Insert new Data into SE +############################ +db.execute(""" + select ProbeSet.%s, ProbeSetXRef.DataId from ProbeSet, ProbeSetXRef + where ProbeSet.Id=ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId=%d""" + % (IdStr, ProbeSetFreezeId)) +results = db.fetchall() + +ProbeNameId = {} +for Name, Id in results: + ProbeNameId[Name] = Id + +ferror = open("ProbeError.txt", "wb") + +DataValues = [] + +fp.seek(0) # XZ add this line +line = fp.readline() # XZ add this line +line = fp.readline() + +kj = 0 +while line: + line2 = string.split(string.strip(line), '\t') + line2 = list(map(string.strip, line2)) + + CellId = line2[0] + if CellId not in ProbeNameId: + ferror.write(CellId + " doesn't exist\n") + else: + DataId = ProbeNameId[CellId] + datasorig = line2[dataStart:] + + i = 0 + for item in datasorig: + if item != '': + value = '('+str(DataId)+','+str(Ids[i])+','+str(item)+')' + DataValues.append(value) + i += 1 + + kj += 1 + if kj % 100 == 0: + Dataitems = ','.join(DataValues) + cmd = 'insert ProbeSetSE values %s' % Dataitems + db.execute(cmd) + + DataValues = [] + line = fp.readline() + print((CellId, " doesn't exist")) + print(('inserted ', kj, ' lines')) + print(('used ', time.time()-time0, ' seconds')) + +if len(DataValues) > 0: + DataValues = ','.join(DataValues) + cmd = 'insert ProbeSetSE values %s' % DataValues + db.execute(cmd) + +con.close() diff --git a/setup.py b/setup.py index a9b71fab..8436dcd3 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ setup(name='genenetwork2', url = "https://github.com/genenetwork/genenetwork2/blob/master/README.md", description = 'Website and tools for genetics.', include_package_data=True, - packages=['wqflask','etc'], + packages=['wqflask', 'etc'], scripts=['bin/genenetwork2'], # package_data = { # 'etc': ['*.py'] diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py index 12057203..5e16a5cd 100644 --- a/test/requests/link_checker.py +++ b/test/requests/link_checker.py @@ -23,12 +23,9 @@ def is_in_page_link(link): return pattern.match(link) def get_links(doc): - return filter( - lambda x: not ( + return [x for x in [y.get("href") for y in doc.cssselect("a")] if not ( is_root_link(x) - or is_mailto_link(x)) - , map(lambda y: y.get("href") - , doc.cssselect("a"))) + or is_mailto_link(x))] def verify_link(link): if link[0] == "#": @@ -57,9 +54,9 @@ def check_page(host, start_url): print("Checking links host "+host+" in page `"+start_url+"`") doc = parse(start_url).getroot() links = get_links(doc) - in_page_links = filter(is_in_page_link, links) - internal_links = filter(is_internal_link, links) - external_links = filter(lambda x: not (is_internal_link(x) or is_in_page_link(x)), links) + in_page_links = list(filter(is_in_page_link, links)) + internal_links = list(filter(is_internal_link, links)) + external_links = [x for x in links if not (is_internal_link(x) or is_in_page_link(x))] for link in internal_links: verify_link(host+link) diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 0fccaab3..707569db 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -33,7 +33,7 @@ class GeneralObject: def __init__(self, *args, **kw): self.contents = list(args) - for name, value in kw.items(): + for name, value in list(kw.items()): setattr(self, name, value) def __setitem__(self, key, value): @@ -50,16 +50,16 @@ class GeneralObject: def __str__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): if key != 'contents': s += '%s = %s\n' % (key, self.__dict__[key]) return s def __repr__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): s += '%s = %s\n' % (key, self.__dict__[key]) return s def __cmp__(self, other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) + return len(list(self.__dict__.keys())).__cmp__(len(list(other.__dict__.keys()))) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index cfba9104..8151a29d 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -34,7 +34,6 @@ from utility import webqtlUtil from db import webqtlDatabaseFunction from base import species from base import webqtlConfig -import reaper from flask import Flask, g import os import math @@ -45,7 +44,7 @@ import codecs import json import requests import gzip -import cPickle as pickle +import pickle as pickle import itertools from redis import Redis @@ -254,12 +253,12 @@ class Markers(object): logger.debug("length of self.markers:", len(self.markers)) logger.debug("length of p_values:", len(p_values)) - if type(p_values) is list: + if isinstance(p_values, list): # THIS IS only needed for the case when we are limiting the number of p-values calculated # if len(self.markers) > len(p_values): # self.markers = self.markers[:len(p_values)] - for marker, p_value in itertools.izip(self.markers, p_values): + for marker, p_value in zip(self.markers, p_values): if not p_value: continue marker['p_value'] = float(p_value) @@ -270,7 +269,7 @@ class Markers(object): marker['lod_score'] = -math.log10(marker['p_value']) # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 - elif type(p_values) is dict: + elif isinstance(p_values, dict): filtered_markers = [] for marker in self.markers: #logger.debug("marker[name]", marker['name']) @@ -456,12 +455,7 @@ class DatasetGroup(object): full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) - - if use_reaper: - genotype_1 = reaper.Dataset() - genotype_1.read(full_filename) - else: - genotype_1 = gen_geno_ob.genotype(full_filename) + genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add( diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7666348e..a19b66f7 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -6,7 +6,6 @@ import resource import codecs import requests import random -import urllib from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData @@ -118,7 +117,7 @@ class GeneralTrait(object): vals = [] the_vars = [] sample_aliases = [] - for sample_name, sample_data in self.data.items(): + for sample_name, sample_data in list(self.data.items()): if sample_data.value != None: if not include_variance or sample_data.variance != None: samples.append(sample_name) @@ -193,7 +192,7 @@ class GeneralTrait(object): ''' if self.chr and self.mb: - self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb) + self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) elif self.chr: self.location = 'Chr %s @ Unknown position' % (self.chr) else: @@ -260,7 +259,7 @@ def get_sample_data(): trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text - return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }]) else: return None @@ -440,7 +439,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields,',Geno.') + display_fields_string = string.join(dataset.display_fields, ',Geno.') display_fields_string = 'Geno.' + display_fields_string query = """ SELECT %s @@ -459,7 +458,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) trait_info = g.db.execute(query, - (string.join(dataset.display_fields,','), + (string.join(dataset.display_fields, ','), dataset.type, trait.name)).fetchone() if trait_info: @@ -605,6 +604,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError, `trait.name`+' information is not found in the database.' + raise KeyError(repr(trait.name)+' information is not found in the database.') - return trait \ No newline at end of file + return trait diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 1a1b3adc..0971d2a2 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -3,7 +3,10 @@ from flask import g import string -import urllib2 +try: # Python2 support + import urllib.request, urllib.error, urllib.parse +except: + import urllib2 import json from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL from utility.benchmark import Bench @@ -26,8 +29,8 @@ GN_SERVER result when set (which should return a Tuple) else: res2 = result, if LOG_SQL: - logger.debug("Replaced SQL call",query) - logger.debug(path,res2) + logger.debug("Replaced SQL call", query) + logger.debug(path, res2) return res2 else: return fetchone(query) @@ -37,7 +40,7 @@ def fetchone(query): original fetchone, but with logging) """ - with Bench("SQL",LOG_SQL): + with Bench("SQL", LOG_SQL): def helper(query): res = g.db.execute(query) return res.fetchone() @@ -48,7 +51,7 @@ def fetchall(query): original fetchall, but with logging) """ - with Bench("SQL",LOG_SQL): + with Bench("SQL", LOG_SQL): def helper(query): res = g.db.execute(query) return res.fetchall() @@ -58,8 +61,12 @@ def gn_server(path): """Return JSON record by calling GN_SERVER """ - with Bench("GN_SERVER",LOG_SQL): - res = urllib2.urlopen(GN_SERVER_URL+path) + with Bench("GN_SERVER", LOG_SQL): + res = () + try: + res = urllib.request.urlopen(GN_SERVER_URL+path) + except: + res = urllib2.urlopen(GN_SERVER_URL+path) rest = res.read() res2 = json.loads(rest) logger.debug(res2) diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 8a9dc79d..2805febd 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -35,13 +35,13 @@ def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0] - logger.debug("retrieve_species result:",result) + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0] + logger.debug("retrieve_species result:", result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0] - logger.debug("retrieve_species_id result:",result) + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0] + logger.debug("retrieve_species_id result:", result) return result diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..fd65a52a 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -41,7 +41,7 @@ from __future__ import print_function, division import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -50,7 +50,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI import MySQLdb import simplejson as json -import urlparse +import urllib.parse #import sqlalchemy as sa @@ -66,7 +66,7 @@ from pprint import pformat as pf def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -108,7 +108,7 @@ def get_types(groups): """Build types list""" types = {} #print("Groups: ", pf(groups)) - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code @@ -195,9 +195,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b7b2dc8e..4231cc7c 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -82,7 +82,7 @@ def get_probeset_vals(cursor, dataset_name): def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) - first_probeset = list(probeset_vals.itervalues())[0] + first_probeset = list(probeset_vals.values())[0] print("\n**** first_probeset is:", pf(first_probeset)) for strain in strains: print("\n**** strain is:", pf(strain)) diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 41a3aad8..4d6e03bf 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,12 +1,12 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.insert(0,'./') +sys.path.insert(0, './') + -from itertools import izip import MySQLdb -import urlparse +import urllib.parse import numpy as np import pandas as pd @@ -22,7 +22,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -37,7 +37,7 @@ def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) - input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=range(1, ncols)) + input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) #This function taken from https://github.com/ShawnLYU/Quantile_Normalize @@ -60,7 +60,7 @@ def set_data(dataset_name): sample_list = [] with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh: - for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)): + for i, (line1, line2) in enumerate(zip(orig_fh, quant_fh)): trait_dict = {} sample_list = [] if i == 0: diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 54fd8e7e..abd5416c 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -22,7 +22,7 @@ import sys import json # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -34,7 +34,7 @@ Redis = get_redis_conn() import MySQLdb -import urlparse +import urllib.parse from utility.logger import getLogger logger = getLogger(__name__) @@ -42,7 +42,7 @@ logger = getLogger(__name__) def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py index adffdca3..58108e03 100644 --- a/wqflask/run_gunicorn.py +++ b/wqflask/run_gunicorn.py @@ -7,7 +7,7 @@ # from flask import Flask # application = Flask(__name__) -print "===> Starting up Gunicorn process" +print("===> Starting up Gunicorn process") from wqflask import app from utility.startup_config import app_config diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index b9b71129..7d9d7649 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -54,7 +54,7 @@ def cformat(d, rank=0): strD = "%2.6f" % d if rank == 0: - while strD[-1] in ('0','.'): + while strD[-1] in ('0', '.'): if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: break elif strD[-1] == '.': @@ -82,7 +82,7 @@ def frange(start, end=None, inc=1.0): # Need to adjust the count. AFAICT, it always comes up one short. count += 1 L = [start] * count - for i in xrange(1, count): + for i in range(1, count): L[i] = start + i * inc return L @@ -93,7 +93,7 @@ def find_outliers(vals): >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) (11.252500000000001, 0.5364999999999993) - >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) + >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) (32.0, -8.0) If there are no vals, returns None for the upper and lower bounds, @@ -158,7 +158,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab j = int((item-xLow)/step) Count[j] += 1 - yLow, yTop, stepY=detScale(0,max(Count)) + yLow, yTop, stepY=detScale(0, max(Count)) #draw data xScale = plotWidth/(xTop-xLow) @@ -170,7 +170,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab xc = (dataXY[i]-xLow)*xScale+xLeftOffset yc =-(count-yLow)*yScale+yTopOffset+plotHeight im_drawer.rectangle( - xy=((xc+2,yc),(xc+barWidth-2,yTopOffset+plotHeight)), + xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)), outline=barColor, fill=barColor) #draw drawing region @@ -179,81 +179,81 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab ) #draw scale - scaleFont=ImageFont.truetype(font=COUR_FILE,size=11) + scaleFont=ImageFont.truetype(font=COUR_FILE, size=11) x=xLow for i in range(int(stepX)+1): xc=xLeftOffset+(x-xLow)*xScale im_drawer.line( - xy=((xc,yTopOffset+plotHeight),(xc,yTopOffset+plotHeight+5)), + xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)), fill=axesColor) strX = cformat(d=x, rank=0) im_drawer.text( text=strX, - xy=(xc-im_drawer.textsize(strX,font=scaleFont)[0]/2, - yTopOffset+plotHeight+14),font=scaleFont) + xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2, + yTopOffset+plotHeight+14), font=scaleFont) x+= (xTop - xLow)/stepX y=yLow for i in range(int(stepY)+1): yc=yTopOffset+plotHeight-(y-yLow)*yScale - im_drawer.line(xy=((xLeftOffset,yc),(xLeftOffset-5,yc)), fill=axesColor) + im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor) strY = "%d" %y im_drawer.text( text=strY, - xy=(xLeftOffset-im_drawer.textsize(strY,font=scaleFont)[0]-6,yc+5), + xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5), font=scaleFont) y+= (yTop - yLow)/stepY #draw label - labelFont=ImageFont.truetype(font=TAHOMA_FILE,size=17) + labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17) if XLabel: im_drawer.text( text=XLabel, xy=(xLeftOffset+( - plotWidth-im_drawer.textsize(XLabel,font=labelFont)[0])/2.0, + plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0, yTopOffset+plotHeight+yBottomOffset-10), - font=labelFont,fill=labelColor) + font=labelFont, fill=labelColor) if YLabel: draw_rotated_text(canvas, text=YLabel, xy=(19, yTopOffset+plotHeight-( plotHeight-im_drawer.textsize( - YLabel,font=labelFont)[0])/2.0), + YLabel, font=labelFont)[0])/2.0), font=labelFont, fill=labelColor, angle=90) - labelFont=ImageFont.truetype(font=VERDANA_FILE,size=16) + labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16) if title: im_drawer.text( text=title, xy=(xLeftOffset+(plotWidth-im_drawer.textsize( - title,font=labelFont)[0])/2.0, + title, font=labelFont)[0])/2.0, 20), - font=labelFont,fill=labelColor) + font=labelFont, fill=labelColor) # This function determines the scale of the plot -def detScaleOld(min,max): +def detScaleOld(min, max): if min>=max: return None elif min == -1.0 and max == 1.0: - return [-1.2,1.2,12] + return [-1.2, 1.2, 12] else: a=max-min b=floor(log10(a)) - c=pow(10.0,b) + c=pow(10.0, b) if a < c*5.0: c/=2.0 #print a,b,c low=c*floor(min/c) high=c*ceil(max/c) - return [low,high,round((high-low)/c)] + return [low, high, round((high-low)/c)] def detScale(min=0,max=0): if min>=max: return None elif min == -1.0 and max == 1.0: - return [-1.2,1.2,12] + return [-1.2, 1.2, 12] else: a=max-min if max != 0: @@ -265,7 +265,7 @@ def detScale(min=0,max=0): min -= 0.1*a a=max-min b=floor(log10(a)) - c=pow(10.0,b) + c=pow(10.0, b) low=c*floor(min/c) high=c*ceil(max/c) n = round((high-low)/c) @@ -283,7 +283,7 @@ def detScale(min=0,max=0): high=c*ceil(max/c) n = round((high-low)/c) - return [low,high,n] + return [low, high, n] def bluefunc(x): return 1.0 / (1.0 + exp(-10*(x-0.6))) @@ -292,7 +292,7 @@ def redfunc(x): return 1.0 / (1.0 + exp(10*(x-0.5))) def greenfunc(x): - return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3) + return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3) def colorSpectrum(n=100): multiple = 10 diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index d9856eed..204ff59a 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -19,7 +19,7 @@ class Struct(object): ''' def __init__(self, obj): - for k, v in obj.iteritems(): + for k, v in list(obj.items()): if isinstance(v, dict): setattr(self, k, Struct(v)) else: @@ -30,6 +30,6 @@ class Struct(object): def __repr__(self): return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for - (k, v) in self.__dict__.iteritems())) + (k, v) in list(self.__dict__.items()))) diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index ece7022c..bc03eb55 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -17,7 +17,7 @@ logger = logging.getLogger(__name__ ) def check_resource_availability(dataset, trait_id=None): #At least for now assume temporary entered traits are accessible - if type(dataset) == str: + if isinstance(dataset, str): return webqtlConfig.DEFAULT_PRIVILEGES if dataset.type == "Temp": return webqtlConfig.DEFAULT_PRIVILEGES diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 8f1c916b..221e5151 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -38,9 +38,9 @@ class Bench(object): @classmethod def report(cls): - total_time = sum((time_taken for time_taken in cls.entries.itervalues())) + total_time = sum((time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") - for name, time_taken in cls.entries.iteritems(): + for name, time_taken in list(cls.entries.items()): percent = int(round((time_taken/total_time) * 100)) print("[{}%] {}: {}".format(percent, name, time_taken)) print() diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 15cdd0bc..a5580811 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -59,7 +59,7 @@ def get_elasticsearch_connection(for_user=True): try: assert(ELASTICSEARCH_HOST) assert(ELASTICSEARCH_PORT) - logger.info("ES HOST",ELASTICSEARCH_HOST) + logger.info("ES HOST", ELASTICSEARCH_HOST) es = Elasticsearch([{ "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 23b0b650..ae42f834 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -175,7 +175,7 @@ class Locus(object): start_pos = 3 for allele in marker_row[start_pos:]: - if allele in geno_table.keys(): + if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U") \ No newline at end of file diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 9ce809b6..9a4a235a 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -13,7 +13,7 @@ logger = logging.getLogger(__name__ ) def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" - if "temp_trait" in start_vars.keys(): + if "temp_trait" in list(start_vars.keys()): if start_vars['temp_trait'] == "True": self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) else: diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 510b1041..e904eb94 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -42,10 +42,10 @@ class GNLogger: """ - def __init__(self,name): + def __init__(self, name): self.logger = logging.getLogger(name) - def setLevel(self,value): + def setLevel(self, value): """Set the undelying log level""" self.logger.setLevel(value) @@ -54,7 +54,7 @@ class GNLogger: level=num to filter on LOG_LEVEL_DEBUG. """ - self.collect(self.logger.debug,*args) + self.collect(self.logger.debug, *args) def debug20(self,*args): """Call logging.debug for multiple args. Use level=num to filter on @@ -63,15 +63,15 @@ LOG_LEVEL_DEBUG (NYI). """ if level <= LOG_LEVEL_DEBUG: if self.logger.getEffectiveLevel() < 20: - self.collect(self.logger.debug,*args) + self.collect(self.logger.debug, *args) def info(self,*args): """Call logging.info for multiple args""" - self.collect(self.logger.info,*args) + self.collect(self.logger.info, *args) def warning(self,*args): """Call logging.warning for multiple args""" - self.collect(self.logger.warning,*args) + self.collect(self.logger.warning, *args) # self.logger.warning(self.collect(*args)) def error(self,*args): @@ -79,13 +79,13 @@ LOG_LEVEL_DEBUG (NYI). now = datetime.datetime.utcnow() time_str = now.strftime('%H:%M:%S UTC %Y%m%d') l = [time_str]+list(args) - self.collect(self.logger.error,*l) + self.collect(self.logger.error, *l) def infof(self,*args): """Call logging.info for multiple args lazily""" # only evaluate function when logging if self.logger.getEffectiveLevel() < 30: - self.collectf(self.logger.debug,*args) + self.collectf(self.logger.debug, *args) def debugf(self,level=0,*args): """Call logging.debug for multiple args lazily and handle @@ -95,15 +95,15 @@ LOG_LEVEL_DEBUG (NYI). # only evaluate function when logging if level <= LOG_LEVEL_DEBUG: if self.logger.getEffectiveLevel() < 20: - self.collectf(self.logger.debug,*args) + self.collectf(self.logger.debug, *args) def sql(self, sqlcommand, fun = None): """Log SQL command, optionally invoking a timed fun""" if LOG_SQL: caller = stack()[1][3] - if caller in ['fetchone','fetch1','fetchall']: + if caller in ['fetchone', 'fetch1', 'fetchall']: caller = stack()[2][3] - self.info(caller,sqlcommand) + self.info(caller, sqlcommand) if fun: result = fun(sqlcommand) if LOG_SQL: @@ -119,7 +119,7 @@ LOG_LEVEL_DEBUG (NYI). if isinstance(a, str): out = out + a else: - out = out + pf(a,width=160) + out = out + pf(a, width=160) fun(out) def collectf(self,fun,*args): @@ -134,7 +134,7 @@ LOG_LEVEL_DEBUG (NYI). if isinstance(a, str): out = out + a else: - out = out + pf(a,width=160) + out = out + pf(a, width=160) fun(out) # Get the module logger. You can override log levels at the diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index 0c2ce7af..c486abba 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -12,9 +12,9 @@ WHITE = ImageColor.getrgb("white") def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): # type: (Image, str, ImageFont, tuple, ImageColor, int) """Utility function draw rotated text""" - tmp_img = Image.new("RGBA", font.getsize(text), color=(0,0,0,0)) + tmp_img = Image.new("RGBA", font.getsize(text), color=(0, 0, 0, 0)) draw_text = ImageDraw.Draw(tmp_img) - draw_text.text(text=text, xy=(0,0), font=font, fill=fill) + draw_text.text(text=text, xy=(0, 0), font=font, fill=fill) tmp_img2 = tmp_img.rotate(angle, expand=1) tmp_img2.save("/{0}/{1}.png".format(TEMPDIR, text), format="png") canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy])) diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 817284dd..f1aaebb6 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -27,7 +27,7 @@ def app_config(): port = get_setting_int("SERVER_PORT") if get_setting_bool("USE_GN_SERVER"): - print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") + print(("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")) import requests page = requests.get(get_setting("GN_SERVER_URL")) if page.status_code != 200: @@ -36,4 +36,4 @@ def app_config(): # import utility.elasticsearch_tools as es # es.test_elasticsearch_connection() - print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) + print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index db13b9d1..b92cc2d1 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -25,54 +25,56 @@ # Last updated by GeneNetwork Core Team 2010/10/20 #!/usr/bin/env python -##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) -##All rights reserved. +# Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) +# All rights reserved. ## -##Redistribution and use in source and binary forms, with or without modification, -##are permitted provided that the following conditions are met: +# Redistribution and use in source and binary forms, with or without modification, +# are permitted provided that the following conditions are met: ## -##Redistributions of source code must retain the above copyright notice, this -##list of conditions and the following disclaimer. +# Redistributions of source code must retain the above copyright notice, this +# list of conditions and the following disclaimer. ## -##Redistributions in binary form must reproduce the above copyright notice, -##this list of conditions and the following disclaimer in the documentation and/or -##other materials provided with the distribution. +# Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation and/or +# other materials provided with the distribution. ## -##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of -##its contributors may be used to endorse or promote products derived from this -##software without specific prior written permission. +# Neither the name of the Stichting Farmaceutische Kengetallen nor the names of +# its contributors may be used to endorse or promote products derived from this +# software without specific prior written permission. ## -##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE -##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE +# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# Thanks to Gerald Rosennfellner for his help and useful comments. -##Thanks to Gerald Rosennfellner for his help and useful comments. - -__doc__="""Use SVGdraw to generate your SVGdrawings. +import sys +import exceptions +__doc__ = """Use SVGdraw to generate your SVGdrawings. SVGdraw uses an object model drawing and a method toXML to create SVG graphics by using easy to use classes and methods usualy you start by creating a drawing eg d=drawing() - #then you create a SVG root element + # then you create a SVG root element s=svg() - #then you add some elements eg a circle and add it to the svg root element + # then you add some elements eg a circle and add it to the svg root element c=circle() - #you can supply attributes by using named arguments. + # you can supply attributes by using named arguments. c=circle(fill='red',stroke='blue') - #or by updating the attributes attribute: + # or by updating the attributes attribute: c.attributes['stroke-width']=1 s.addElement(c) - #then you add the svg root element to the drawing + # then you add the svg root element to the drawing d.setSVG(s) - #and finaly you xmlify the drawing + # and finaly you xmlify the drawing d.toXml() @@ -82,7 +84,7 @@ This module was created using the SVG specification of www.w3c.org and the O'Reilly (www.oreilly.com) python books as information sources. A svg viewer is available from www.adobe.com""" -__version__="1.0" +__version__ = "1.0" # there are two possibilities to generate svg: # via a dom implementation and directly using <element>text</element> strings @@ -93,33 +95,34 @@ __version__="1.0" # Note that PyXML is required for using the dom implementation. # It is also possible to use the standard minidom. But I didn't try that one. # Anyway the text based approach is about 60 times faster than using the full dom implementation. -use_dom_implementation=0 +use_dom_implementation = 0 -import exceptions -if use_dom_implementation<>0: +if use_dom_implementation != 0: try: from xml.dom import implementation from xml.dom.ext import PrettyPrint except: - raise exceptions.ImportError, "PyXML is required for using the dom implementation" -#The implementation is used for the creating the XML document. -#The prettyprint module is used for converting the xml document object to a xml file + raise exceptions.ImportError( + "PyXML is required for using the dom implementation") +# The implementation is used for the creating the XML document. +# The prettyprint module is used for converting the xml document object to a xml file + +assert sys.version_info[0] >= 2 +if sys.version_info[1] < 2: + True = 1 + False = 0 + file = open + +sys.setrecursionlimit = 50 +# The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) +# won't eat up too much processor time. + +# the following code is pasted form xml.sax.saxutils +# it makes it possible to run the code without the xml sax package installed +# To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts + -import sys -assert sys.version_info[0]>=2 -if sys.version_info[1]<2: - True=1 - False=0 - file=open - -sys.setrecursionlimit=50 -#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) -#won't eat up too much processor time. - -#the following code is pasted form xml.sax.saxutils -#it makes it possible to run the code without the xml sax package installed -#To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts def _escape(data, entities={}): """Escape &, <, and > in a string of data. @@ -127,13 +130,14 @@ def _escape(data, entities={}): the optional entities parameter. The keys and values must all be strings; each key will be replaced with its corresponding value. """ - #data = data.replace("&", "&") + # data = data.replace("&", "&") data = data.replace("<", "<") data = data.replace(">", ">") - for chars, entity in entities.items(): + for chars, entity in list(entities.items()): data = data.replace(chars, entity) return data + def _quoteattr(data, entities={}): """Escape and quote an attribute value. @@ -156,96 +160,121 @@ def _quoteattr(data, entities={}): return data - def _xypointlist(a): """formats a list of xy pairs""" - s='' - for e in a: #this could be done more elegant - s+=str(e)[1:-1] +' ' + s = '' + for e in a: # this could be done more elegant + s += str(e)[1:-1] + ' ' return s + def _viewboxlist(a): """formats a tuple""" - s='' + s = '' for e in a: - s+=str(e)+' ' + s += str(e)+' ' return s + def _pointlist(a): """formats a list of numbers""" return str(a)[1:-1] + class pathdata: """class used to create a pathdata object which can be used for a path. although most methods are pretty straightforward it might be useful to look at the SVG specification.""" - #I didn't test the methods below. - def __init__(self,x=None,y=None): - self.path=[] + # I didn't test the methods below. + + def __init__(self, x=None, y=None): + self.path = [] if x is not None and y is not None: self.path.append('M '+str(x)+' '+str(y)) + def closepath(self): """ends the path""" self.path.append('z') - def move(self,x,y): + + def move(self, x, y): """move to absolute""" self.path.append('M '+str(x)+' '+str(y)) - def relmove(self,x,y): + + def relmove(self, x, y): """move to relative""" self.path.append('m '+str(x)+' '+str(y)) - def line(self,x,y): + + def line(self, x, y): """line to absolute""" self.path.append('L '+str(x)+' '+str(y)) - def relline(self,x,y): + + def relline(self, x, y): """line to relative""" self.path.append('l '+str(x)+' '+str(y)) - def hline(self,x): + + def hline(self, x): """horizontal line to absolute""" self.path.append('H'+str(x)) - def relhline(self,x): + + def relhline(self, x): """horizontal line to relative""" self.path.append('h'+str(x)) - def vline(self,y): + + def vline(self, y): """verical line to absolute""" self.path.append('V'+str(y)) - def relvline(self,y): + + def relvline(self, y): """vertical line to relative""" self.path.append('v'+str(y)) - def bezier(self,x1,y1,x2,y2,x,y): + + def bezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy absolut""" - self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relbezier(self,x1,y1,x2,y2,x,y): + self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2) + + ','+str(y2)+' '+str(x)+','+str(y)) + + def relbezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy relative""" - self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def smbezier(self,x2,y2,x,y): + self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2) + + ','+str(y2)+' '+str(x)+','+str(y)) + + def smbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy absolut""" self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relsmbezier(self,x2,y2,x,y): + + def relsmbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy relative""" self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def qbezier(self,x1,y1,x,y): + + def qbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy absolut""" self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def relqbezier(self,x1,y1,x,y): + + def relqbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy relative""" self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def smqbezier(self,x,y): + + def smqbezier(self, x, y): """smooth quadratic bezier to xy absolut""" self.path.append('T'+str(x)+','+str(y)) - def relsmqbezier(self,x,y): + + def relsmqbezier(self, x, y): """smooth quadratic bezier to xy relative""" self.path.append('t'+str(x)+','+str(y)) - def ellarc(self,rx,ry,xrot,laf,sf,x,y): + + def ellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) - def relellarc(self,rx,ry,xrot,laf,sf,x,y): + self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot) + + ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + + def relellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative""" - self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot) + + ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + def __repr__(self): return ' '.join(self.path) - - class SVGelement: """SVGelement(type,attributes,elements,text,namespace,**args) Creates a arbitrary svg element and is intended to be subclassed not used on its own. @@ -256,52 +285,56 @@ class SVGelement: namespace. Note the elements==None, if elements = None:self.elements=[] construction. This is done because if you default to elements=[] every object has a reference to the same empty list.""" - def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args): - self.type=type - if attributes==None: - self.attributes={} + + def __init__(self, type='', attributes=None, elements=None, text='', namespace='', cdata=None, **args): + self.type = type + if attributes == None: + self.attributes = {} else: - self.attributes=attributes - if elements==None: - self.elements=[] + self.attributes = attributes + if elements == None: + self.elements = [] else: - self.elements=elements - self.text=text - self.namespace=namespace - self.cdata=cdata - for arg in args.keys(): + self.elements = elements + self.text = text + self.namespace = namespace + self.cdata = cdata + for arg in list(args.keys()): arg2 = arg.replace("__", ":") arg2 = arg2.replace("_", "-") - self.attributes[arg2]=args[arg] - def addElement(self,SVGelement): + self.attributes[arg2] = args[arg] + + def addElement(self, SVGelement): """adds an element to a SVGelement SVGelement.addElement(SVGelement) """ self.elements.append(SVGelement) - def toXml(self,level,f): + def toXml(self, level, f): f.write('\t'*level) f.write('<'+self.type) - for attkey in self.attributes.keys(): - f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey]))) + for attkey in list(self.attributes.keys()): + f.write(' '+_escape(str(attkey))+'=' + + _quoteattr(str(self.attributes[attkey]))) if self.namespace: - f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"') + f.write(' xmlns="' + _escape(str(self.namespace)) + + '" xmlns:xlink="http://www.w3.org/1999/xlink"') if self.elements or self.text or self.cdata: f.write('>') if self.elements: f.write('\n') for element in self.elements: - element.toXml(level+1,f) + element.toXml(level+1, f) if self.cdata: f.write('\n'+'\t'*(level+1)+'<![CDATA[') for line in self.cdata.splitlines(): f.write('\n'+'\t'*(level+2)+line) f.write('\n'+'\t'*(level+1)+']]>\n') if self.text: - if type(self.text)==type(''): #If the text is only text + if isinstance(self.text, type('')): # If the text is only text f.write(_escape(str(self.text))) - else: #If the text is a spannedtext class + else: # If the text is a spannedtext class f.write(str(self.text)) if self.elements: f.write('\t'*level+'</'+self.type+'>\n') @@ -312,6 +345,7 @@ class SVGelement: else: f.write('/>\n') + class tspan(SVGelement): """ts=tspan(text='',**args) @@ -323,19 +357,22 @@ class tspan(SVGelement): st.addtspan(ts) t=text(3,5,st) """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'tspan',**args) - if self.text<>None: - self.text=text + + def __init__(self, text=None, **args): + SVGelement.__init__(self, 'tspan', **args) + if self.text != None: + self.text = text + def __repr__(self): - s="<tspan" - for key,value in self.attributes.items(): - s+= ' %s="%s"' % (key,value) - s+='>' - s+=self.text - s+='</tspan>' + s = "<tspan" + for key, value in list(self.attributes.items()): + s += ' %s="%s"' % (key, value) + s += '>' + s += self.text + s += '</tspan>' return s + class tref(SVGelement): """tr=tref(link='',**args) @@ -346,16 +383,19 @@ class tref(SVGelement): st.addtref(tr) t=text(3,5,st) """ - def __init__(self,link,**args): - SVGelement.__init__(self,'tref',{'xlink:href':link},**args) + + def __init__(self, link, **args): + SVGelement.__init__(self, 'tref', {'xlink:href': link}, **args) + def __repr__(self): - s="<tref" + s = "<tref" - for key,value in self.attributes.items(): - s+= ' %s="%s"' % (key,value) - s+='/>' + for key, value in list(self.attributes.items()): + s += ' %s="%s"' % (key, value) + s += '/>' return s + class spannedtext: """st=spannedtext(textlist=[]) @@ -374,46 +414,49 @@ class spannedtext: st.addtext('This text is not bold') t=text(3,5,st) """ - def __init__(self,textlist=None): - if textlist==None: - self.textlist=[] + + def __init__(self, textlist=None): + if textlist == None: + self.textlist = [] else: - self.textlist=textlist - def addtext(self,text=''): + self.textlist = textlist + + def addtext(self, text=''): self.textlist.append(text) - def addtspan(self,tspan): + + def addtspan(self, tspan): self.textlist.append(tspan) - def addtref(self,tref): + + def addtref(self, tref): self.textlist.append(tref) + def __repr__(self): - s="" + s = "" for element in self.textlist: - s+=str(element) + s += str(element) return s + class rect(SVGelement): """r=rect(width,height,x,y,fill,stroke,stroke_width,**args) a rectangle is defined by a width and height and a xy pair """ - def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args): - if width==None or height==None: - if width<>None: - raise ValueError, 'height is required' - if height<>None: - raise ValueError, 'width is required' - else: - raise ValueError, 'both height and width are required' - SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) - if x<>None: + + def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args): + if width == None or height == None: + raise ValueError('both height and width are required') + + SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args) + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width class ellipse(SVGelement): @@ -423,22 +466,18 @@ class ellipse(SVGelement): """ def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): if rx==None or ry== None: - if rx<>None: - raise ValueError, 'rx is required' - if ry<>None: - raise ValueError, 'ry is required' - else: - raise ValueError, 'both rx and ry are required' - SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) - if cx<>None: + raise ValueError('both rx and ry are required') + + SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args) + if cx!=None: self.attributes['cx']=cx - if cy<>None: + if cy!=None: self.attributes['cy']=cy - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width @@ -449,17 +488,17 @@ class circle(SVGelement): """ def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): if r==None: - raise ValueError, 'r is required' - SVGelement.__init__(self,'circle',{'r':r},**args) - if cx<>None: + raise ValueError('r is required') + SVGelement.__init__(self, 'circle', {'r':r}, **args) + if cx!=None: self.attributes['cx']=cx - if cy<>None: + if cy!=None: self.attributes['cy']=cy - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width class point(circle): @@ -469,7 +508,7 @@ class point(circle): very small rectangle if you use many points because a circle is difficult to render. """ def __init__(self,x,y,fill='black',**args): - circle.__init__(self,x,y,1,fill,**args) + circle.__init__(self, x, y, 1, fill, **args) class line(SVGelement): """l=line(x1,y1,x2,y2,stroke,stroke_width,**args) @@ -477,18 +516,18 @@ class line(SVGelement): A line is defined by a begin x,y pair and an end x,y pair """ def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'line',**args) - if x1<>None: + SVGelement.__init__(self, 'line', **args) + if x1!=None: self.attributes['x1']=x1 - if y1<>None: + if y1!=None: self.attributes['y1']=y1 - if x2<>None: + if x2!=None: self.attributes['x2']=x2 - if y2<>None: + if y2!=None: self.attributes['y2']=y2 - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke class polyline(SVGelement): @@ -497,12 +536,12 @@ class polyline(SVGelement): a polyline is defined by a list of xy pairs """ def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args) - if fill<>None: + SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args) + if fill!=None: self.attributes['fill']=fill - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke class polygon(SVGelement): @@ -511,12 +550,12 @@ class polygon(SVGelement): a polygon is defined by a list of xy pairs """ def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args) - if fill<>None: + SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args) + if fill!=None: self.attributes['fill']=fill - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke class path(SVGelement): @@ -525,14 +564,14 @@ class path(SVGelement): a path is defined by a path object and optional width, stroke and fillcolor """ def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args): - SVGelement.__init__(self,'path',{'d':str(pathdata)},**args) - if stroke<>None: + SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args) + if stroke!=None: self.attributes['stroke']=stroke - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if id<>None: + if id!=None: self.attributes['id']=id @@ -542,18 +581,18 @@ class text(SVGelement): a text element can bge used for displaying text on the screen """ def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args): - SVGelement.__init__(self,'text',**args) - if x<>None: + SVGelement.__init__(self, 'text', **args) + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if font_size<>None: + if font_size!=None: self.attributes['font-size']=font_size - if font_family<>None: + if font_family!=None: self.attributes['font-family']=font_family - if text<>None: + if text!=None: self.text=text - if text_anchor<>None: + if text_anchor!=None: self.attributes['text-anchor']=text_anchor @@ -563,8 +602,8 @@ class textpath(SVGelement): a textpath places a text on a path which is referenced by a link. """ def __init__(self,link,text=None,**args): - SVGelement.__init__(self,'textPath',{'xlink:href':link},**args) - if text<>None: + SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args) + if text!=None: self.text=text class pattern(SVGelement): @@ -575,16 +614,16 @@ class pattern(SVGelement): in x and y to cover the areas to be painted. """ def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args): - SVGelement.__init__(self,'pattern',**args) - if x<>None: + SVGelement.__init__(self, 'pattern', **args) + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if width<>None: + if width!=None: self.attributes['width']=width - if height<>None: + if height!=None: self.attributes['height']=height - if patternUnits<>None: + if patternUnits!=None: self.attributes['patternUnits']=patternUnits class title(SVGelement): @@ -594,8 +633,8 @@ class title(SVGelement): add at least one to the root svg element """ def __init__(self,text=None,**args): - SVGelement.__init__(self,'title',**args) - if text<>None: + SVGelement.__init__(self, 'title', **args) + if text!=None: self.text=text class description(SVGelement): @@ -605,8 +644,8 @@ class description(SVGelement): Add this element before adding other elements. """ def __init__(self,text=None,**args): - SVGelement.__init__(self,'desc',**args) - if text<>None: + SVGelement.__init__(self, 'desc', **args) + if text!=None: self.text=text class lineargradient(SVGelement): @@ -616,16 +655,16 @@ class lineargradient(SVGelement): stop elements van be added to define the gradient colors. """ def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): - SVGelement.__init__(self,'linearGradient',**args) - if x1<>None: + SVGelement.__init__(self, 'linearGradient', **args) + if x1!=None: self.attributes['x1']=x1 - if y1<>None: + if y1!=None: self.attributes['y1']=y1 - if x2<>None: + if x2!=None: self.attributes['x2']=x2 - if y2<>None: + if y2!=None: self.attributes['y2']=y2 - if id<>None: + if id!=None: self.attributes['id']=id class radialgradient(SVGelement): @@ -635,18 +674,18 @@ class radialgradient(SVGelement): stop elements van be added to define the gradient colors. """ def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args): - SVGelement.__init__(self,'radialGradient',**args) - if cx<>None: + SVGelement.__init__(self, 'radialGradient', **args) + if cx!=None: self.attributes['cx']=cx - if cy<>None: + if cy!=None: self.attributes['cy']=cy - if r<>None: + if r!=None: self.attributes['r']=r - if fx<>None: + if fx!=None: self.attributes['fx']=fx - if fy<>None: + if fy!=None: self.attributes['fy']=fy - if id<>None: + if id!=None: self.attributes['id']=id class stop(SVGelement): @@ -655,8 +694,8 @@ class stop(SVGelement): Puts a stop color at the specified radius """ def __init__(self,offset,stop_color=None,**args): - SVGelement.__init__(self,'stop',{'offset':offset},**args) - if stop_color<>None: + SVGelement.__init__(self, 'stop', {'offset':offset}, **args) + if stop_color!=None: self.attributes['stop-color']=stop_color class style(SVGelement): @@ -665,7 +704,7 @@ class style(SVGelement): Add a CDATA element to this element for defing in line stylesheets etc.. """ def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args) + SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args) class image(SVGelement): @@ -675,16 +714,11 @@ class image(SVGelement): """ def __init__(self,url,x=None,y=None,width=None,height=None,**args): if width==None or height==None: - if width<>None: - raise ValueError, 'height is required' - if height<>None: - raise ValueError, 'width is required' - else: - raise ValueError, 'both height and width are required' - SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) - if x<>None: + raise ValueError('both height and width are required') + SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args) + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y class cursor(SVGelement): @@ -693,7 +727,7 @@ class cursor(SVGelement): defines a custom cursor for a element or a drawing """ def __init__(self,url,**args): - SVGelement.__init__(self,'cursor',{'xlink:href':url},**args) + SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args) class marker(SVGelement): @@ -703,18 +737,18 @@ class marker(SVGelement): add an element to it which should be used as a marker. """ def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args): - SVGelement.__init__(self,'marker',**args) - if id<>None: + SVGelement.__init__(self, 'marker', **args) + if id!=None: self.attributes['id']=id - if viewBox<>None: + if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) - if refx<>None: + if refx!=None: self.attributes['refX']=refx - if refy<>None: + if refy!=None: self.attributes['refY']=refy - if markerWidth<>None: + if markerWidth!=None: self.attributes['markerWidth']=markerWidth - if markerHeight<>None: + if markerHeight!=None: self.attributes['markerHeight']=markerHeight class group(SVGelement): @@ -724,8 +758,8 @@ class group(SVGelement): g.addElement(SVGelement) """ def __init__(self,id=None,**args): - SVGelement.__init__(self,'g',**args) - if id<>None: + SVGelement.__init__(self, 'g', **args) + if id!=None: self.attributes['id']=id class symbol(SVGelement): @@ -738,10 +772,10 @@ class symbol(SVGelement): """ def __init__(self,id=None,viewBox=None,**args): - SVGelement.__init__(self,'symbol',**args) - if id<>None: + SVGelement.__init__(self, 'symbol', **args) + if id!=None: self.attributes['id']=id - if viewBox<>None: + if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) class defs(SVGelement): @@ -750,7 +784,7 @@ class defs(SVGelement): container for defining elements """ def __init__(self,**args): - SVGelement.__init__(self,'defs',**args) + SVGelement.__init__(self, 'defs', **args) class switch(SVGelement): """sw=switch(**args) @@ -760,7 +794,7 @@ class switch(SVGelement): Refer to the SVG specification for details. """ def __init__(self,**args): - SVGelement.__init__(self,'switch',**args) + SVGelement.__init__(self, 'switch', **args) class use(SVGelement): @@ -769,15 +803,15 @@ class use(SVGelement): references a symbol by linking to its id and its position, height and width """ def __init__(self,link,x=None,y=None,width=None,height=None,**args): - SVGelement.__init__(self,'use',{'xlink:href':link},**args) - if x<>None: + SVGelement.__init__(self, 'use', {'xlink:href':link}, **args) + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if width<>None: + if width!=None: self.attributes['width']=width - if height<>None: + if height!=None: self.attributes['height']=height @@ -788,15 +822,15 @@ class link(SVGelement): a.addElement(SVGelement) """ def __init__(self,link='',**args): - SVGelement.__init__(self,'a',{'xlink:href':link},**args) + SVGelement.__init__(self, 'a', {'xlink:href':link}, **args) class view(SVGelement): """v=view(id,**args) a view can be used to create a view with different attributes""" def __init__(self,id=None,**args): - SVGelement.__init__(self,'view',**args) - if id<>None: + SVGelement.__init__(self, 'view', **args) + if id!=None: self.attributes['id']=id class script(SVGelement): @@ -806,7 +840,7 @@ class script(SVGelement): """ def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args) + SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args) class animate(SVGelement): """an=animate(attribute,from,to,during,**args) @@ -814,12 +848,12 @@ class animate(SVGelement): animates an attribute. """ def __init__(self,attribute,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animate',{'attributeName':attribute},**args) - if fr<>None: + SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args) + if fr!=None: self.attributes['from']=fr - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur class animateMotion(SVGelement): @@ -828,10 +862,10 @@ class animateMotion(SVGelement): animates a SVGelement over the given path in dur seconds """ def __init__(self,pathdata,dur,**args): - SVGelement.__init__(self,'animateMotion',**args) - if pathdata<>None: + SVGelement.__init__(self, 'animateMotion', **args) + if pathdata!=None: self.attributes['path']=str(pathdata) - if dur<>None: + if dur!=None: self.attributes['dur']=dur class animateTransform(SVGelement): @@ -840,15 +874,15 @@ class animateTransform(SVGelement): transform an element from and to a value. """ def __init__(self,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args) - #As far as I know the attributeName is always transform - if type<>None: + SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args) + # As far as I know the attributeName is always transform + if type!=None: self.attributes['type']=type - if fr<>None: + if fr!=None: self.attributes['from']=fr - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur class animateColor(SVGelement): """ac=animateColor(attribute,type,from,to,dur,**args) @@ -856,14 +890,14 @@ class animateColor(SVGelement): Animates the color of a element """ def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args) - if type<>None: + SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args) + if type!=None: self.attributes['type']=type - if fr<>None: + if fr!=None: self.attributes['from']=fr - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur class set(SVGelement): """st=set(attribute,to,during,**args) @@ -871,10 +905,10 @@ class set(SVGelement): sets an attribute to a value for a """ def __init__(self,attribute,to=None,dur=None,**args): - SVGelement.__init__(self,'set',{'attributeName':attribute},**args) - if to<>None: + SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args) + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur @@ -895,12 +929,12 @@ class svg(SVGelement): d.toXml() """ def __init__(self,viewBox=None, width=None, height=None,**args): - SVGelement.__init__(self,'svg',**args) - if viewBox<>None: + SVGelement.__init__(self, 'svg', **args) + if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) - if width<>None: + if width!=None: self.attributes['width']=width - if height<>None: + if height!=None: self.attributes['height']=height self.namespace="http://www.w3.org/2000/svg" @@ -918,27 +952,27 @@ class drawing: def __init__(self, entity={}): self.svg=None self.entity = entity - def setSVG(self,svg): + def setSVG(self, svg): self.svg=svg - #Voeg een element toe aan de grafiek toe. + # Voeg een element toe aan de grafiek toe. if use_dom_implementation==0: def toXml(self, filename='',compress=False): - import cStringIO - xml=cStringIO.StringIO() + import io + xml=io.StringIO() xml.write("<?xml version='1.0' encoding='UTF-8'?>\n") xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"") if self.entity: xml.write(" [\n") - for item in self.entity.keys(): + for item in list(self.entity.keys()): xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item])) xml.write("]") xml.write(">\n") - self.svg.toXml(0,xml) + self.svg.toXml(0, xml) if not filename: if compress: import gzip - f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') + f=io.StringIO() + zf=gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -948,11 +982,11 @@ class drawing: else: if filename[-4:]=='svgz': import gzip - f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9) + f=gzip.GzipFile(filename=filename, mode="wb", compresslevel=9) f.write(xml.getvalue()) f.close() else: - f=file(filename,'w') + f=file(filename, 'w') f.write(xml.getvalue()) f.close() @@ -963,40 +997,40 @@ class drawing: writes a svg drawing to the screen or to a file compresses if filename ends with svgz or if compress is true """ - doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') + doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') global root - #root is defined global so it can be used by the appender. Its also possible to use it as an arugument but - #that is a bit messy. - root=implementation.createDocument(None,None,doctype) - #Create the xml document. + # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but + # that is a bit messy. + root=implementation.createDocument(None, None, doctype) + # Create the xml document. global appender - def appender(element,elementroot): + def appender(element, elementroot): """This recursive function appends elements to an element and sets the attributes and type. It stops when alle elements have been appended""" if element.namespace: - e=root.createElementNS(element.namespace,element.type) + e=root.createElementNS(element.namespace, element.type) else: e=root.createElement(element.type) if element.text: textnode=root.createTextNode(element.text) e.appendChild(textnode) - for attribute in element.attributes.keys(): #in element.attributes is supported from python 2.2 - e.setAttribute(attribute,str(element.attributes[attribute])) + for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2 + e.setAttribute(attribute, str(element.attributes[attribute])) if element.elements: for el in element.elements: - e=appender(el,e) + e=appender(el, e) elementroot.appendChild(e) return elementroot - root=appender(self.svg,root) + root=appender(self.svg, root) if not filename: - import cStringIO - xml=cStringIO.StringIO() - PrettyPrint(root,xml) + import io + xml=io.StringIO() + PrettyPrint(root, xml) if compress: import gzip - f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') + f=io.StringIO() + zf=gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -1007,23 +1041,23 @@ class drawing: try: if filename[-4:]=='svgz': import gzip - import cStringIO - xml=cStringIO.StringIO() - PrettyPrint(root,xml) - f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9) + import io + xml=io.StringIO() + PrettyPrint(root, xml) + f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9) f.write(xml.getvalue()) f.close() else: - f=open(filename,'w') - PrettyPrint(root,f) + f=open(filename, 'w') + PrettyPrint(root, f) f.close() except: - print "Cannot write SVG file: " + filename + print(("Cannot write SVG file: " + filename)) def validate(self): try: import xml.parsers.xmlproc.xmlval except: - raise exceptions.ImportError,'PyXml is required for validating SVG' + raise exceptions.ImportError('PyXml is required for validating SVG') svg=self.toXml() xv=xml.parsers.xmlproc.xmlval.XMLValidator() try: @@ -1031,38 +1065,38 @@ class drawing: except: raise Exception("SVG is not well formed, see messages above") else: - print "SVG well formed" + print("SVG well formed") if __name__=='__main__': d=drawing() - s=svg((0,0,100,100)) - r=rect(-100,-100,300,300,'cyan') + s=svg((0, 0, 100, 100)) + r=rect(-100, -100, 300, 300, 'cyan') s.addElement(r) t=title('SVGdraw Demo') s.addElement(t) g=group('animations') - e=ellipse(0,0,5,2) + e=ellipse(0, 0, 5, 2) g.addElement(e) - c=circle(0,0,1,'red') + c=circle(0, 0, 1, 'red') g.addElement(c) - pd=pathdata(0,-10) + pd=pathdata(0, -10) for i in range(6): - pd.relsmbezier(10,5,0,10) - pd.relsmbezier(-10,5,0,10) - an=animateMotion(pd,10) + pd.relsmbezier(10, 5, 0, 10) + pd.relsmbezier(-10, 5, 0, 10) + an=animateMotion(pd, 10) an.attributes['rotate']='auto-reverse' an.attributes['repeatCount']="indefinite" g.addElement(an) s.addElement(g) - for i in range(20,120,20): - u=use('#animations',i,0) + for i in range(20, 120, 20): + u=use('#animations', i, 0) s.addElement(u) - for i in range(0,120,20): - for j in range(5,105,10): - c=circle(i,j,1,'red','black',.5) + for i in range(0, 120, 20): + for j in range(5, 105, 10): + c=circle(i, j, 1, 'red', 'black', .5) s.addElement(c) d.setSVG(s) - print d.toXml() + print((d.toXml())) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 5bf700c9..2f2726c6 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -20,6 +20,6 @@ class TempData(object): if __name__ == "__main__": redis = Redis() - for key in redis.keys(): + for key in list(redis.keys()): for field in redis.hkeys(key): print("{}.{}={}".format(key, field, redis.hget(key, field))) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 77db5d53..68ef0f04 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -15,7 +15,7 @@ OVERRIDES = {} def app_set(command_id, value): """Set application wide value""" - app.config.setdefault(command_id,value) + app.config.setdefault(command_id, value) return value def get_setting(command_id,guess=None): @@ -45,7 +45,7 @@ def get_setting(command_id,guess=None): def value(command): if command: # sys.stderr.write("Found "+command+"\n") - app_set(command_id,command) + app_set(command_id, command) return command else: return None @@ -68,7 +68,7 @@ def get_setting(command_id,guess=None): def get_setting_bool(id): v = get_setting(id) - if v not in [0,False,'False','FALSE',None]: + if v not in [0, False, 'False', 'FALSE', None]: return True return False @@ -108,16 +108,16 @@ def js_path(module=None): raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" def reaper_command(guess=None): - return get_setting("REAPER_COMMAND",guess) + return get_setting("REAPER_COMMAND", guess) def gemma_command(guess=None): - return assert_bin(get_setting("GEMMA_COMMAND",guess)) + return assert_bin(get_setting("GEMMA_COMMAND", guess)) def gemma_wrapper_command(guess=None): - return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess)) + return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess)) def plink_command(guess=None): - return assert_bin(get_setting("PLINK_COMMAND",guess)) + return assert_bin(get_setting("PLINK_COMMAND", guess)) def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") @@ -180,7 +180,7 @@ def locate(name, subdir=None): raise Exception("Can not locate "+name+" in "+base) def locate_phewas(name, subdir=None): - return locate(name,'/phewas/'+subdir) + return locate(name, '/phewas/'+subdir) def locate_ignore_error(name, subdir=None): """ @@ -204,7 +204,7 @@ def tempdir(): """ Get UNIX TMPDIR by default """ - return valid_path(get_setting("TMPDIR","/tmp")) + return valid_path(get_setting("TMPDIR", "/tmp")) BLUE = '\033[94m' GREEN = '\033[92m' @@ -214,20 +214,20 @@ ENDC = '\033[0m' def show_settings(): from utility.tools import LOG_LEVEL - print("Set global log level to "+BLUE+LOG_LEVEL+ENDC) + print(("Set global log level to "+BLUE+LOG_LEVEL+ENDC)) log_level = getattr(logging, LOG_LEVEL.upper()) logging.basicConfig(level=log_level) logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******" - keylist = app.config.keys() + keylist = list(app.config.keys()) + print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******") keylist.sort() for k in keylist: try: - print("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)) + print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC))) except: - print("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)) + print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC))) # Cached values @@ -279,10 +279,10 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT') SMTP_USERNAME = get_setting('SMTP_USERNAME') SMTP_PASSWORD = get_setting('SMTP_PASSWORD') -REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command()) -GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command()) assert(GEMMA_COMMAND is not None) -PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) +PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) @@ -295,11 +295,11 @@ assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher")) +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") -JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) +JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 53661ae4..d4979011 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -41,22 +41,22 @@ ParInfo ={ 'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'], 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], -'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'], -'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'], +'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], +'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], 'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], 'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], 'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'], +'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'], 'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], 'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], 'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], 'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], 'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'], 'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'], -'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'], -'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'], -'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'], -'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'], +'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'], +'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'], +'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'], +'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'], 'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] } @@ -64,7 +64,7 @@ ParInfo ={ # Accessory Functions ######################################### -def genRandStr(prefix = "", length=8, chars=string.letters+string.digits): +def genRandStr(prefix = "", length=8, chars=string.ascii_letters+string.digits): from random import choice _str = prefix[:] for i in range(length): @@ -91,7 +91,7 @@ def readLineCSV(line): ### dcrowell July 2008 returnList[0]=returnList[0][1:] return returnList -def cmpEigenValue(A,B): +def cmpEigenValue(A, B): try: if A[0] > B[0]: return -1 @@ -107,7 +107,7 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users) if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: access_to_confidential_phenotype_trait = 1 else: - AuthorizedUsersList=map(string.strip, string.split(authorized_users, ',')) + AuthorizedUsersList=list(map(string.strip, string.split(authorized_users, ','))) if AuthorizedUsersList.__contains__(userName): access_to_confidential_phenotype_trait = 1 - return access_to_confidential_phenotype_trait \ No newline at end of file + return access_to_confidential_phenotype_trait diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index 7f5312c1..eb05645e 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -36,7 +36,7 @@ def do_correlation(start_vars): #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) final_results = [] - for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]): + for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]): if corr_params['type'] == "tissue": [sample_r, num_overlap, sample_p, symbol] = corr_results[trait] result_dict = { @@ -76,20 +76,20 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): if corr_params['type'] == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature" trait_geneid_dict = this_dataset.retrieve_genes("GeneId") corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) else: - for target_trait, target_vals in target_dataset.trait_data.iteritems(): + for target_trait, target_vals in list(target_dataset.trait_data.items()): result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) if result is not None: corr_results[target_trait] = result - sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) return sorted_results @@ -100,10 +100,10 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values()) + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values())) tissue_corr_data = {} - for trait, symbol in trait_symbol_dict.iteritems(): + for trait, symbol in list(trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] @@ -119,7 +119,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) lit_corr_data = {} - for trait, gene_id in trait_geneid_dict.iteritems(): + for trait, gene_id in list(trait_geneid_dict.items()): mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index fedf3e0b..41966f78 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -61,7 +61,7 @@ def get_types(groups): """Build types list""" types = {} - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name, _family_name in group_dict: if phenotypes_exist(group_name): @@ -136,9 +136,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 6324cabe..5f9b81b8 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -6,7 +6,7 @@ import os, io, csv, json, datetime, requests, yaml import zlib from zipfile import ZipFile, ZIP_DEFLATED -import StringIO +import io import flask from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, send_file @@ -308,7 +308,7 @@ def fetch_traits(dataset_name, file_format = "json"): else: filename = dataset_name + "_trait_ids.csv" - si = StringIO.StringIO() + si = io.StringIO() csv_writer = csv.writer(si) csv_writer.writerows([[trait_id] for trait_id in trait_ids]) output = make_response(si.getvalue()) @@ -322,7 +322,7 @@ def fetch_traits(dataset_name, file_format = "json"): else: filename = dataset_name + "_trait_names.csv" - si = StringIO.StringIO() + si = io.StringIO() csv_writer = csv.writer(si) csv_writer.writerows([[trait_name] for trait_name in trait_names]) output = make_response(si.getvalue()) @@ -413,7 +413,7 @@ def fetch_traits(dataset_name, file_format = "json"): for result in g.db.execute(final_query).fetchall(): results_list.append(result) - si = StringIO.StringIO() + si = io.StringIO() csv_writer = csv.writer(si) csv_writer.writerows(results_list) output = make_response(si.getvalue()) @@ -517,9 +517,9 @@ def all_sample_data(dataset_name, file_format = "csv"): line_list.append("x") results_list.append(line_list) - results_list = map(list, zip(*results_list)) + results_list = list(map(list, zip(*results_list))) - si = StringIO.StringIO() + si = io.StringIO() csv_writer = csv.writer(si) csv_writer.writerows(results_list) output = make_response(si.getvalue()) @@ -558,10 +558,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - "sample_name" : sample[0], - "sample_name_2" : sample[1], - "value" : sample[2], - "data_id" : sample[3], + "sample_name": sample[0], + "sample_name_2": sample[1], + "value": sample[2], + "data_id": sample[3], } if sample[4]: sample_dict["se"] = sample[4] @@ -706,7 +706,7 @@ def get_mapping_results(): if format == "csv": filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv" - si = StringIO.StringIO() + si = io.StringIO() csv_writer = csv.writer(si) csv_writer.writerows(results) output = make_response(si.getvalue()) @@ -732,7 +732,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): if request.args['limit_to'].isdigit(): limit_num = int(request.args['limit_to']) - si = StringIO.StringIO() + si = io.StringIO() if file_format == "csv" or file_format == "geno": filename = group_name + ".geno" diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 42a09fed..d77567f8 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -10,7 +10,7 @@ import uuid import hashlib import base64 -import urlparse +import urllib.parse import simplejson as json @@ -193,7 +193,7 @@ def view_collection(): params = request.args uc_id = params['uc_id'] - uc = (collection for collection in g.user_session.user_collections if collection["id"] == uc_id).next() + uc = next((collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) traits = uc["members"] trait_obs = [] diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 09d6b9cc..3e5daa50 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -24,7 +24,7 @@ import sys # sys.path.append(".") Never do this in a webserver! import string -import cPickle +import pickle import os import time import pp diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 819836b1..57a8d85f 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -36,13 +36,13 @@ class CorrScatterPlot(object): samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data) self.data = [] - self.indIDs = samples_1.keys() + self.indIDs = list(samples_1.keys()) vals_1 = [] - for sample in samples_1.keys(): + for sample in list(samples_1.keys()): vals_1.append(samples_1[sample].value) self.data.append(vals_1) vals_2 = [] - for sample in samples_2.keys(): + for sample in list(samples_2.keys()): vals_2.append(samples_2[sample].value) self.data.append(vals_2) diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index 06dec795..abaa212f 100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -50,12 +50,12 @@ from flask import Flask, g def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pearson'): - R_primary = rpy2.robjects.FloatVector(range(len(primaryValue))) + R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue)))) N = len(primaryValue) for i in range(len(primaryValue)): R_primary[i] = primaryValue[i] - R_target = rpy2.robjects.FloatVector(range(len(targetValue))) + R_target = rpy2.robjects.FloatVector(list(range(len(targetValue)))) for i in range(len(targetValue)): R_target[i]=targetValue[i] diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index de7a1c0c..233a3a03 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -20,22 +20,11 @@ from __future__ import absolute_import, print_function, division -import sys - -import string -import cPickle -import os -import time -import pp -import math import collections -import resource import json - import scipy import numpy import rpy2.robjects as ro # R Objects -import rpy2.rinterface as ri from rpy2.robjects.packages import importr utils = importr("utils") @@ -108,17 +97,17 @@ class CorrelationResults(object): self.sample_data = {} self.corr_type = start_vars['corr_type'] self.corr_method = start_vars['corr_sample_method'] - self.min_expr = get_float(start_vars,'min_expr') - self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0) - self.p_range_upper = get_float(start_vars,'p_range_upper',1.0) + self.min_expr = get_float(start_vars, 'min_expr') + self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0) + self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0) if ('loc_chr' in start_vars and 'min_loc_mb' in start_vars and 'max_loc_mb' in start_vars): - self.location_chr = get_string(start_vars,'loc_chr') - self.min_location_mb = get_int(start_vars,'min_loc_mb') - self.max_location_mb = get_int(start_vars,'max_loc_mb') + self.location_chr = get_string(start_vars, 'loc_chr') + self.min_location_mb = get_int(start_vars, 'min_loc_mb') + self.max_location_mb = get_int(start_vars, 'max_loc_mb') else: self.location_chr = self.min_location_mb = self.max_location_mb = None @@ -145,10 +134,10 @@ class CorrelationResults(object): if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( self.dataset.group.parlist + self.dataset.group.f1list)] - self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples) + self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples) self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) - self.target_dataset.get_trait_data(self.sample_data.keys()) + self.target_dataset.get_trait_data(list(self.sample_data.keys())) self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) @@ -168,41 +157,41 @@ class CorrelationResults(object): tissue_corr_data = self.do_tissue_correlation_for_all_traits() if tissue_corr_data != None: - for trait in tissue_corr_data.keys()[:self.return_number]: + for trait in list(tissue_corr_data.keys())[:self.return_number]: self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) else: - for trait, values in self.target_dataset.trait_data.iteritems(): + for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) elif self.corr_type == "lit": self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId") lit_corr_data = self.do_lit_correlation_for_all_traits() - for trait in lit_corr_data.keys()[:self.return_number]: + for trait in list(lit_corr_data.keys())[:self.return_number]: self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": - for trait, values in self.target_dataset.trait_data.iteritems(): + for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) - self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), + self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()), key=lambda t: -abs(t[1][0]))) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert min/max chromosome to an int for the location range option range_chr_as_int = None - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if 'loc_chr' in start_vars: if chr_info.name == self.location_chr: range_chr_as_int = order_id - for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): + for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option chr_as_int = 0 - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if chr_info.name == trait_object.chr: chr_as_int = order_id @@ -297,14 +286,14 @@ class CorrelationResults(object): #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=self.trait_symbol_dict.values()) + symbol_list=list(self.trait_symbol_dict.values())) #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) #print("trait_gene_symbols: ", pf(trait_gene_symbols)) tissue_corr_data = {} - for trait, symbol in self.trait_symbol_dict.iteritems(): + for trait, symbol in list(self.trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] @@ -314,7 +303,7 @@ class CorrelationResults(object): tissue_corr_data[trait] = [symbol, result[0], result[2]] - tissue_corr_data = collections.OrderedDict(sorted(tissue_corr_data.items(), + tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()), key=lambda t: -abs(t[1][1]))) return tissue_corr_data @@ -359,7 +348,7 @@ class CorrelationResults(object): input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) lit_corr_data = {} - for trait, gene_id in self.trait_geneid_dict.iteritems(): + for trait, gene_id in list(self.trait_geneid_dict.items()): mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: @@ -387,7 +376,7 @@ class CorrelationResults(object): else: lit_corr_data[trait] = [gene_id, 0] - lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(), + lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()), key=lambda t: -abs(t[1][1]))) return lit_corr_data @@ -648,4 +637,4 @@ def get_header_fields(data_type, corr_method): 'N', 'Sample p(r)'] - return header_fields \ No newline at end of file + return header_fields diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 0ac94139..ea786289 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -24,7 +24,7 @@ import sys # sys.path.append(".") Never do this in a webserver! import string -import cPickle +import pickle import os import datetime import time @@ -42,6 +42,10 @@ import rpy2.robjects as robjects from pprint import pformat as pf from utility.redis_tools import get_redis_conn +try: # Only import this for Python3 + from functools import reduce +except: + pass Redis = get_redis_conn() THIRTY_DAYS = 60 * 60 * 24 * 30 @@ -190,7 +194,7 @@ class CorrelationMatrix(object): if self.do_PCA == True: self.pca_works = "True" self.pca_trait_ids = [] - pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) + pca = self.calculate_pca(list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) self.loadings_array = self.process_loadings() else: self.pca_works = "False" @@ -199,8 +203,8 @@ class CorrelationMatrix(object): self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, - cols = range(len(self.traits)), - rows = range(len(self.traits)), + cols = list(range(len(self.traits))), + rows = list(range(len(self.traits))), samples = self.all_sample_list, sample_data = self.sample_data,) # corr_results = [result[1] for result in result_row for result_row in self.corr_results]) @@ -271,14 +275,14 @@ def zScore(trait_data_array): i = 0 for data in trait_data_array: N = len(data) - S = reduce(lambda x,y: x+y, data, 0.) - SS = reduce(lambda x,y: x+y*y, data, 0.) + S = reduce(lambda x, y: x+y, data, 0.) + SS = reduce(lambda x, y: x+y*y, data, 0.) mean = S/N var = SS - S*S/N stdev = math.sqrt(var/(N-1)) if stdev == 0: stdev = 1e-100 - data2 = map(lambda x:(x-mean)/stdev,data) + data2 = [(x-mean)/stdev for x in data] trait_data_array[i] = data2 i += 1 return trait_data_array @@ -290,7 +294,7 @@ def sortEigenVectors(vector): combines = [] i = 0 for item in eigenValues: - combines.append([eigenValues[i],eigenVectors[i]]) + combines.append([eigenValues[i], eigenVectors[i]]) i += 1 combines.sort(webqtlUtil.cmpEigenValue) A = [] @@ -298,8 +302,8 @@ def sortEigenVectors(vector): for item in combines: A.append(item[0]) B.append(item[1]) - sum = reduce(lambda x,y: x+y, A, 0.0) - A = map(lambda x:x*100.0/sum, A) + sum = reduce(lambda x, y: x+y, A, 0.0) + A = [x*100.0/sum for x in A] return [A, B] except: - return [] \ No newline at end of file + return [] diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 35067036..e58a7b87 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -125,7 +125,7 @@ class CTL(object): gt = create_trait(name = ts[0], dataset_name = ts[1]) gt = retrieve_sample_data(gt, dataset, individuals) for ind in individuals: - if ind in gt.data.keys(): + if ind in list(gt.data.keys()): traits.append(gt.data[ind].value) else: traits.append("-999") @@ -175,7 +175,7 @@ class CTL(object): sys.stdout.flush() # Create the interactive graph for cytoscape visualization (Nodes and Edges) - if not type(significant) == ri.RNULLType: + if not isinstance(significant, ri.RNULLType): for x in range(len(significant[0])): logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console tsS = significant[0][x].split(':') # Source diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 1e15d28f..cc9c1860 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -46,8 +46,8 @@ class DoSearch(object): def handle_wildcard(self, str): keyword = str.strip() - keyword = keyword.replace("*",".*") - keyword = keyword.replace("?",".") + keyword = keyword.replace("*", ".*") + keyword = keyword.replace("?", ".") return keyword diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 3272c03d..2f4e9aac 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -2,7 +2,7 @@ from __future__ import print_function, division import csv import xlsxwriter -import StringIO +import io import datetime import itertools @@ -61,9 +61,9 @@ def export_search_results_csv(targs): traits_by_group = sort_traits_by_group(trait_list) file_list = [] - for group in traits_by_group.keys(): + for group in list(traits_by_group.keys()): group_traits = traits_by_group[group] - buff = StringIO.StringIO() + buff = io.StringIO() writer = csv.writer(buff) csv_rows = [] @@ -122,7 +122,7 @@ def export_search_results_csv(targs): csv_rows.append(row_contents) - csv_rows = map(list, itertools.izip_longest(*[row for row in csv_rows])) + csv_rows = list(map(list, itertools.zip_longest(*[row for row in csv_rows]))) writer.writerows(csv_rows) csv_data = buff.getvalue() buff.close() @@ -135,7 +135,7 @@ def export_search_results_csv(targs): def sort_traits_by_group(trait_list=[]): traits_by_group = {} for trait in trait_list: - if trait.dataset.group.name not in traits_by_group.keys(): + if trait.dataset.group.name not in list(traits_by_group.keys()): traits_by_group[trait.dataset.group.name] = [] traits_by_group[trait.dataset.group.name].append(trait) diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 7a5dba73..9844bab4 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -54,10 +54,10 @@ class SendToGeneWeaver(object): trait_name_list = get_trait_name_list(self.trait_list) self.hidden_vars = { - 'client' : "genenetwork", - 'species' : species_name, - 'idtype' : self.chip_name, - 'list' : string.join(trait_name_list, ","), + 'client': "genenetwork", + 'species': species_name, + 'idtype': self.chip_name, + 'list': string.join(trait_name_list, ","), } def get_trait_name_list(trait_list): diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 5098a184..4fdc1f13 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -4,7 +4,7 @@ import sys # sys.path.append(".") Never in a running webserver import string -import cPickle +import pickle import os import datetime import time @@ -30,7 +30,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR from MySQLdb import escape_string as escape -import cPickle as pickle +import pickle as pickle import simplejson as json from pprint import pformat as pf @@ -60,7 +60,7 @@ class Heatmap(object): chrnames = [] self.species = species.TheSpecies(dataset=self.trait_list[0][1]) - for key in self.species.chromosomes.chromosomes.keys(): + for key in list(self.species.chromosomes.chromosomes.keys()): chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) for trait_db in self.trait_list: @@ -93,7 +93,7 @@ class Heatmap(object): pos = [] markernames = [] - for trait in self.trait_results.keys(): + for trait in list(self.trait_results.keys()): lodnames.append(trait) self.dataset.group.get_markers() diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 2c60dd70..a39e5d0f 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -24,7 +24,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): ##List current Species and other Species speciesId = speciesDict[species] - otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys()) + otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())] otherSpecies.remove([species, speciesId]) results = g.db.execute(""" diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index a92adb90..255e3b74 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -47,7 +47,11 @@ from base.webqtlConfig import GENERATED_IMAGE_DIR from utility.pillow_utils import draw_rotated_text, draw_open_polygon import utility.logger -logger = utility.logger.getLogger(__name__) +try: # Only import this for Python3 + from functools import reduce +except: + pass +logger = utility.logger.getLogger(__name__ ) RED = ImageColor.getrgb("red") BLUE = ImageColor.getrgb("blue") @@ -265,7 +269,7 @@ class DisplayMappingResults(object): self.manhattan_plot = start_vars['manhattan_plot'] - if 'permCheck' in start_vars.keys(): + if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] else: self.permChecked = False @@ -278,46 +282,46 @@ class DisplayMappingResults(object): else: self.nperm = 0 - if 'bootCheck' in start_vars.keys(): + if 'bootCheck' in list(start_vars.keys()): self.bootChecked = start_vars['bootCheck'] else: self.bootChecked = False - if 'num_bootstrap' in start_vars.keys(): + if 'num_bootstrap' in list(start_vars.keys()): self.nboot = int(start_vars['num_bootstrap']) else: self.nboot = 0 - if 'bootstrap_results' in start_vars.keys(): + if 'bootstrap_results' in list(start_vars.keys()): self.bootResult = start_vars['bootstrap_results'] else: self.bootResult = [] - if 'do_control' in start_vars.keys(): + if 'do_control' in list(start_vars.keys()): self.doControl = start_vars['do_control'] else: self.doControl = "false" - if 'control_marker' in start_vars.keys(): + if 'control_marker' in list(start_vars.keys()): self.controlLocus = start_vars['control_marker'] else: self.controlLocus = "" - if 'covariates' in start_vars.keys(): + if 'covariates' in list(start_vars.keys()): self.covariates = start_vars['covariates'] - if 'maf' in start_vars.keys(): + if 'maf' in list(start_vars.keys()): self.maf = start_vars['maf'] else: self.maf = "" - if 'output_files' in start_vars.keys(): + if 'output_files' in list(start_vars.keys()): self.output_files = start_vars['output_files'] - if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma": + if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper": + if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] if 'output_files' in start_vars: self.output_files = ",".join(start_vars['output_files']) self.categorical_vars = "" self.perm_strata = "" - if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys(): + if 'perm_strata' in list(start_vars.keys()) and 'categorical_vars' in list(start_vars.keys()): self.categorical_vars = start_vars['categorical_vars'] self.perm_strata = start_vars['perm_strata'] @@ -359,7 +363,7 @@ class DisplayMappingResults(object): self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH ## BEGIN HaplotypeAnalyst - if 'haplotypeAnalystCheck' in start_vars.keys(): + if 'haplotypeAnalystCheck' in list(start_vars.keys()): self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck'] else: self.haplotypeAnalystChecked = False @@ -367,25 +371,25 @@ class DisplayMappingResults(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.dominanceChecked = False - if 'LRSCheck' in start_vars.keys(): + if 'LRSCheck' in list(start_vars.keys()): self.LRS_LOD = start_vars['LRSCheck'] else: self.LRS_LOD = start_vars['score_type'] self.intervalAnalystChecked = True self.draw2X = False - if 'additiveCheck' in start_vars.keys(): + if 'additiveCheck' in list(start_vars.keys()): self.additiveChecked = start_vars['additiveCheck'] else: self.additiveChecked = False - if 'viewLegend' in start_vars.keys(): + if 'viewLegend' in list(start_vars.keys()): self.legendChecked = start_vars['viewLegend'] else: self.legendChecked = False - if 'showSNP' in start_vars.keys(): + if 'showSNP' in list(start_vars.keys()): self.SNPChecked = start_vars['showSNP'] else: self.SNPChecked = False - if 'showGenes' in start_vars.keys(): + if 'showGenes' in list(start_vars.keys()): self.geneChecked = start_vars['showGenes'] else: self.geneChecked = False @@ -425,9 +429,9 @@ class DisplayMappingResults(object): Chr_Length.Name in (%s) Order by Chr_Length.OrderId - """ % (self.dataset.group.name, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", "))) + """ % (self.dataset.group.name, string.join(["'%s'" % X[0] for X in self.ChrList[1:]], ", "))) - self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList) + self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList] self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0) if self.ChrLengthMbList: self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval @@ -458,7 +462,7 @@ class DisplayMappingResults(object): else: continue samplelist = list(self.genotype.prgy) - for j,_geno in enumerate (self.genotype[0][1].genotype): + for j, _geno in enumerate (self.genotype[0][1].genotype): for item in smd: if item.name == samplelist[j]: self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 @@ -554,7 +558,7 @@ class DisplayMappingResults(object): #Scales plot differently for high resolution if self.draw2X: - intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2)) + intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2)) gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save( "{}.png".format( @@ -788,17 +792,17 @@ class DisplayMappingResults(object): bootScale = bootScale[:-1] + [highestPercent] bootOffset = 50*fontZoom - bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom) + bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom) im_drawer.rectangle( xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh), - (canvas.size[0]-bootOffset-15*zoom,yZero)), + (canvas.size[0]-bootOffset-15*zoom, yZero)), fill = YELLOW, outline=BLACK) im_drawer.line( xy=((canvas.size[0]-bootOffset+4, yZero), (canvas.size[0]-bootOffset, yZero)), fill=BLACK) TEXT_Y_DISPLACEMENT = -8 - im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+TEXT_Y_DISPLACEMENT), text='0%', + im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%', font=bootScaleFont, fill=BLACK) for item in bootScale: @@ -806,10 +810,10 @@ class DisplayMappingResults(object): continue bootY = yZero-bootHeightThresh*item/highestPercent im_drawer.line( - xy=((canvas.size[0]-bootOffset+4,bootY), - (canvas.size[0]-bootOffset,bootY)), + xy=((canvas.size[0]-bootOffset+4, bootY), + (canvas.size[0]-bootOffset, bootY)), fill=BLACK) - im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+TEXT_Y_DISPLACEMENT), + im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT), text='%2.1f'%item, font=bootScaleFont, fill=BLACK) if self.legendChecked: @@ -818,7 +822,7 @@ class DisplayMappingResults(object): smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) leftOffset = xLeftOffset+(nCol-1)*200 im_drawer.rectangle( - xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)), + xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)), fill=YELLOW, outline=BLACK) im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT), text='Frequency of the Peak LRS', @@ -915,7 +919,7 @@ class DisplayMappingResults(object): TEXT_Y_DISPLACEMENT = -8 im_drawer.text( text="Sequence Site", - xy=(leftOffset+15,startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont, + xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont, fill=self.TOP_RIGHT_INFO_COLOR) def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -965,7 +969,7 @@ class DisplayMappingResults(object): def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1): nameWidths = [] yPaddingTop = 10 - colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12) + colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12) if len(self.qtlresults) >20 and self.selectedChr > -1: rightShift = 20 rightShiftStep = 60 @@ -984,20 +988,20 @@ class DisplayMappingResults(object): rightShift += rightShiftStep name = thisTrait.displayName() - nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont) + nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont) nameWidths.append(nameWidth) im_drawer.rectangle( - xy=((rightShift,yPaddingTop+kstep*15), - (rectWidth+rightShift,yPaddingTop+10+kstep*15)), + xy=((rightShift, yPaddingTop+kstep*15), + (rectWidth+rightShift, yPaddingTop+10+kstep*15)), fill=thisLRSColor, outline=BLACK) im_drawer.text( - text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15), - font=colorFont,fill=BLACK) + text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15), + font=colorFont, fill=BLACK) if thisTrait.db: - COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,) + COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) - Areas = HtmlGenWrapper.create_area_tag(shape='rect',coords=COORDS,href=HREF) + Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF) gifmap.areas.append(Areas) ### TODO def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): @@ -1011,80 +1015,80 @@ class DisplayMappingResults(object): if zoom == 2: fontZoom = 1.5 - labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom) + labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) startPosY = 15 stepPosY = 12*fontZoom if self.manhattan_plot != True: im_drawer.line( - xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)), + xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)), fill=self.LRS_COLOR, width=2) im_drawer.text( - text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+TEXT_Y_DISPLACEMENT), - font=labelFont,fill=BLACK) + text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT), + font=labelFont, fill=BLACK) startPosY += stepPosY if self.additiveChecked: startPosX = xLeftOffset im_drawer.line( - xy=((startPosX,startPosY),(startPosX+17,startPosY)), + xy=((startPosX, startPosY), (startPosX+17, startPosY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=2) im_drawer.line( - xy=((startPosX+18,startPosY),(startPosX+32,startPosY)), + xy=((startPosX+18, startPosY), (startPosX+32, startPosY)), fill=self.ADDITIVE_COLOR_NEGATIVE, width=2) im_drawer.text( - text='Additive Effect',xy=(startPosX+40,startPosY+TEXT_Y_DISPLACEMENT), - font=labelFont,fill=BLACK) + text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT), + font=labelFont, fill=BLACK) if self.genotype.type == 'intercross' and self.dominanceChecked: startPosX = xLeftOffset startPosY += stepPosY im_drawer.line( - xy=((startPosX,startPosY),(startPosX+17,startPosY)), + xy=((startPosX, startPosY), (startPosX+17, startPosY)), fill=self.DOMINANCE_COLOR_POSITIVE, width=4) im_drawer.line( - xy=((startPosX+18,startPosY),(startPosX+35,startPosY)), + xy=((startPosX+18, startPosY), (startPosX+35, startPosY)), fill=self.DOMINANCE_COLOR_NEGATIVE, width=4) im_drawer.text( - text='Dominance Effect', xy=(startPosX+42,startPosY+5), - font=labelFont,fill=BLACK) + text='Dominance Effect', xy=(startPosX+42, startPosY+5), + font=labelFont, fill=BLACK) if self.haplotypeAnalystChecked: startPosY += stepPosY startPosX = xLeftOffset im_drawer.line( - xy=((startPosX,startPosY),(startPosX+17,startPosY)), + xy=((startPosX, startPosY), (startPosX+17, startPosY)), fill=self.HAPLOTYPE_POSITIVE, width=4) im_drawer.line( - xy=((startPosX+18,startPosY),(startPosX+35,startPosY)), + xy=((startPosX+18, startPosY), (startPosX+35, startPosY)), fill=self.HAPLOTYPE_NEGATIVE, width=4) im_drawer.line( - xy=((startPosX+36,startPosY),(startPosX+53,startPosY)), + xy=((startPosX+36, startPosY), (startPosX+53, startPosY)), fill=self.HAPLOTYPE_HETEROZYGOUS, width=4) im_drawer.line( - xy=((startPosX+54,startPosY),(startPosX+67,startPosY)), + xy=((startPosX+54, startPosY), (startPosX+67, startPosY)), fill=self.HAPLOTYPE_RECOMBINATION, width=4) im_drawer.text( text='Haplotypes (Pat, Mat, Het, Unk)', - xy=(startPosX+76,startPosY+5),font=labelFont,fill=BLACK) + xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK) if self.permChecked and self.nperm > 0: startPosY += stepPosY startPosX = xLeftOffset im_drawer.line( - xy=((startPosX, startPosY),( startPosX + 32, startPosY)), + xy=((startPosX, startPosY), ( startPosX + 32, startPosY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) im_drawer.line( - xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)), + xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) im_drawer.text( - text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant), - xy=(xLeftOffset+42,startPosY+TEXT_Y_DISPLACEMENT),font=labelFont,fill=BLACK) + text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant), + xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) im_drawer.text( text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive), - xy=(xLeftOffset+42,startPosY + TEXT_Y_DISPLACEMENT +stepPosY),font=labelFont, + xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont, fill=BLACK) - labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom) + labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom) labelColor = BLACK if self.dataset.type == "Publish" or self.dataset.type == "Geno": dataset_label = self.dataset.fullname @@ -1152,22 +1156,22 @@ class DisplayMappingResults(object): im_drawer.textsize(string2, font=labelFont)[0]) im_drawer.text( text=identification, - xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont, + xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont, fill=labelColor) else: d = 4+ max( im_drawer.textsize(string1, font=labelFont)[0], im_drawer.textsize(string2, font=labelFont)[0]) im_drawer.text( - text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom), - font=labelFont,fill=labelColor) + text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom), + font=labelFont, fill=labelColor) im_drawer.text( - text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom), - font=labelFont,fill=labelColor) + text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom), + font=labelFont, fill=labelColor) if string3 != '': im_drawer.text( - text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom), - font=labelFont,fill=labelColor) + text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom), + font=labelFont, fill=labelColor) def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1194,8 +1198,8 @@ class DisplayMappingResults(object): tenPercentLength = geneLength*0.0001 SNPdensity = theGO["snpCount"]/geneLength - exonStarts = map(float, theGO['exonStarts'].split(",")[:-1]) - exonEnds = map(float, theGO['exonEnds'].split(",")[:-1]) + exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1])) + exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1])) cdsStart = theGO['cdsStart'] cdsEnd = theGO['cdsEnd'] accession = theGO['NM_ID'] @@ -1388,7 +1392,7 @@ class DisplayMappingResults(object): labelText = "3'" im_drawer.text( text=labelText, - xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT), + xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) #draw the genes as rectangles @@ -1541,7 +1545,7 @@ class DisplayMappingResults(object): counter = counter + 1 if item.name == samplelist[k]: ind = counter - maxind=max(ind,maxind) + maxind=max(ind, maxind) # lines if (oldgeno[k] == -1 and _geno == -1): @@ -1710,7 +1714,7 @@ class DisplayMappingResults(object): outline=self.CLICKABLE_WEBQTL_REGION_COLOR, fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": @@ -1732,7 +1736,7 @@ class DisplayMappingResults(object): outline=self.CLICKABLE_PHENOGEN_REGION_COLOR, fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))), + xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT)) @@ -1864,8 +1868,8 @@ class DisplayMappingResults(object): continue Xc = xLeftOffset + plotXScale*(_Mb - startMb) if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark - im_drawer.line(xy=((Xc,yZero), - (Xc,yZero+xMajorTickHeight)), + im_drawer.line(xy=((Xc, yZero), + (Xc, yZero+xMajorTickHeight)), fill=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark labelStr = str(formatStr % _Mb) # What Mbase location to put on the label @@ -1875,8 +1879,8 @@ class DisplayMappingResults(object): text=labelStr, font=MBLabelFont, fill=xAxisLabelColor) else: - im_drawer.line(xy=((Xc,yZero), - (Xc,yZero+xMinorTickHeight)), + im_drawer.line(xy=((Xc, yZero), + (Xc, yZero+xMinorTickHeight)), fill=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark @@ -1909,7 +1913,7 @@ class DisplayMappingResults(object): text="Megabases", xy=( xLeftOffset+(plotWidth-im_drawer.textsize( - "Megabases",font=megabaseLabelFont)[0])/2, + "Megabases", font=megabaseLabelFont)[0])/2, strYLoc+MBLabelFont.font.height+10*(zoom%2)), font=megabaseLabelFont, fill=BLACK) pass @@ -1964,7 +1968,7 @@ class DisplayMappingResults(object): for j, ChrInfo in enumerate(ChrAInfo): preLpos = -1 for i, item in enumerate(ChrInfo): - Lname,Lpos = item + Lname, Lpos = item if Lpos != preLpos: offsetA += stepA differ = 1 @@ -1978,17 +1982,17 @@ class DisplayMappingResults(object): Zorder = 0 if differ: im_drawer.line( - xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\ + xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\ yZero+25)), fill=lineColor) im_drawer.line( - xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\ + xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\ yZero+40+Zorder*(LRectWidth+3))), fill=lineColor) rectColor = ORANGE else: im_drawer.line( - xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\ + xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\ xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))), fill=lineColor) rectColor = DEEPPINK @@ -1996,7 +2000,7 @@ class DisplayMappingResults(object): xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)), (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3)+LRectWidth)), - outline=rectColor,fill=rectColor,width = 0) + outline=rectColor, fill=rectColor, width = 0) COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth) HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno") @@ -2011,7 +2015,7 @@ class DisplayMappingResults(object): ##piddle bug if j == 0: im_drawer.line( - xy=((startPosX,yZero),(startPosX,yZero+40)), + xy=((startPosX, yZero), (startPosX, yZero+40)), fill=lineColor) startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale @@ -2023,7 +2027,7 @@ class DisplayMappingResults(object): strYLoc + MBLabelFont.font.height+ 10*(zoom%2)), font=centimorganLabelFont, fill=BLACK) - im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)), + im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)), fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself @@ -2167,7 +2171,7 @@ class DisplayMappingResults(object): LRS_LOD_Max = 0.000001 yTopOffset + 30*(zoom - 1) yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh - im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)), + im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)), fill=self.LRS_COLOR, width=1*zoom) if all_int: scaleStr = "%d" % item @@ -2243,7 +2247,7 @@ class DisplayMappingResults(object): lrsEdgeWidth = 1 else: if self.additiveChecked: - additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults)) + additiveMax = max([abs(X['additive']) for X in self.qtlresults]) lrsEdgeWidth = 3 if zoom == 2: @@ -2410,7 +2414,7 @@ class DisplayMappingResults(object): im_drawer.text( text="5", xy=( - Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1, + Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1, Yc-4), fill=point_color, font=symbolFont) else: @@ -2477,8 +2481,8 @@ class DisplayMappingResults(object): ) else: im_drawer.line( - xy=((Xc0,yZero-(Yc0-yZero)), - (Xc,yZero-(Yc-yZero))), + xy=((Xc0, yZero-(Yc0-yZero)), + (Xc, yZero-(Yc-yZero))), fill=minusColor, width=lineWidth #, clipX=(xLeftOffset, xLeftOffset + plotWidth) ) @@ -2565,8 +2569,8 @@ class DisplayMappingResults(object): ###draw additive scale if not self.multipleInterval and self.additiveChecked: - additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom) - additiveScale = Plot.detScaleOld(0,additiveMax) + additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom) + additiveScale = Plot.detScaleOld(0, additiveMax) additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) addPlotScale = AdditiveHeightThresh/additiveMax @@ -2576,18 +2580,18 @@ class DisplayMappingResults(object): for item in additiveAxisList: additiveY = yZero - item*addPlotScale im_drawer.line( - xy=((xLeftOffset + plotWidth,additiveY), - (xLeftOffset+4+ plotWidth,additiveY)), + xy=((xLeftOffset + plotWidth, additiveY), + (xLeftOffset+4+ plotWidth, additiveY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) scaleStr = "%2.3f" % item im_drawer.text( text=scaleStr, - xy=(xLeftOffset + plotWidth +6,additiveY+TEXT_Y_DISPLACEMENT), - font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE) + xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT), + font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE) im_drawer.line( - xy=((xLeftOffset+plotWidth,additiveY), - (xLeftOffset+plotWidth,yZero)), + xy=((xLeftOffset+plotWidth, additiveY), + (xLeftOffset+plotWidth, yZero)), fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) im_drawer.line( @@ -2647,7 +2651,7 @@ class DisplayMappingResults(object): chrFontZoom = 2 else: chrFontZoom = 1 - chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom) + chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): @@ -2669,10 +2673,10 @@ class DisplayMappingResults(object): TEXT_Y_DISPLACEMENT = 0 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT), text=_chr.name, font=chrLabelFont, fill=BLACK) - COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20) + COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20) #add by NL 09-03-2010 - HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList) + HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList) #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList) Areas = HtmlGenWrapper.create_area_tag( shape='rect', @@ -2821,7 +2825,7 @@ class DisplayMappingResults(object): else: chr_as_int = int(theGO["Chromosome"]) - 1 if refGene: - literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A") + literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A") this_row = [selectCheck.__str__(), str(tableIterationsCnt), @@ -2959,8 +2963,8 @@ class DisplayMappingResults(object): lCorr = None try: query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s' - for x,y in [(geneId1,geneId2),(geneId2,geneId1)]: - cursor.execute(query,(x,y)) + for x, y in [(geneId1, geneId2), (geneId2, geneId1)]: + cursor.execute(query, (x, y)) lCorr = cursor.fetchone() if lCorr: lCorr = lCorr[0] diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 2f327faf..2f282adc 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -54,7 +54,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): for i, sample in enumerate(ped_sample_list): try: value = vals[i] - value = str(value).replace('value=','') + value = str(value).replace('value=', '') value = value.strip() except: value = -9999 @@ -78,13 +78,13 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): # get strain name from ped file in order def get_samples_from_ped_file(dataset): - ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r") + ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r") line = ped_file.readline() sample_list=[] while line: lineList = string.split(string.strip(line), '\t') - lineList = map(string.strip, lineList) + lineList = list(map(string.strip, lineList)) sample_name = lineList[0] sample_list.append(sample_name) @@ -111,7 +111,7 @@ def parse_plink_output(output_filename, species): line_list = build_line_list(line=line) # only keep the records whose chromosome name is in db - if species.chromosomes.chromosomes.has_key(int(line_list[0])) and line_list[-1] and line_list[-1].strip()!='NA': + if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip()!='NA': chr_name = species.chromosomes.chromosomes[int(line_list[0])] snp = line_list[1] @@ -121,7 +121,7 @@ def parse_plink_output(output_filename, species): if p_value < threshold_p_value: p_value_dict[snp] = float(p_value) - if plink_results.has_key(chr_name): + if chr_name in plink_results: value_list = plink_results[chr_name] # pvalue range is [0,1] @@ -155,8 +155,8 @@ def parse_plink_output(output_filename, species): # output: lineList list ####################################################### def build_line_list(line=None): - line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns - line_list = [item for item in line_list if item <>''] - line_list = map(string.strip, line_list) + line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns + line_list = [item for item in line_list if item !=''] + line_list = list(map(string.strip, line_list)) return line_list \ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 0c560582..189c1985 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -228,4 +228,4 @@ def natural_sort(marker_list): """ convert = lambda text: int(text) if text.isdigit() else text.lower() alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr'])) ] - return sorted(range(len(marker_list)), key = alphanum_key) \ No newline at end of file + return sorted(list(range(len(marker_list))), key = alphanum_key) \ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index c5590a85..0a5758af 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -42,7 +42,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec png = ro.r["png"] # Map the png function dev_off = ro.r["dev.off"] # Map the device off function - print(r_library("qtl")) # Load R/qtl + print((r_library("qtl"))) # Load R/qtl logger.info("QTL library loaded"); diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c9d10f7c..67512bc6 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -18,7 +18,7 @@ import uuid import rpy2.robjects as ro import numpy as np -import cPickle as pickle +import pickle as pickle import itertools import simplejson as json @@ -347,7 +347,7 @@ class RunMapping(object): if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": highest_chr = marker['chr1'] - if 'lod_score' in marker.keys(): + if 'lod_score' in list(marker.keys()): self.qtl_results.append(marker) self.trimmed_markers = results @@ -411,7 +411,7 @@ class RunMapping(object): if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] - if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): + if ('lod_score' in list(marker.keys())) or ('lrs_value' in list(marker.keys())): self.qtl_results.append(marker) with Bench("Exporting Results"): @@ -538,28 +538,28 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Mb," + score_type) else: output_file.write("Cm," + score_type) - if "additive" in markers[0].keys(): + if "additive" in list(markers[0].keys()): output_file.write(",Additive") - if "dominance" in markers[0].keys(): + if "dominance" in list(markers[0].keys()): output_file.write(",Dominance") output_file.write("\n") for i, marker in enumerate(markers): output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",") - if "lod_score" in marker.keys(): + if "lod_score" in list(marker.keys()): output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) - if "additive" in marker.keys(): + if "additive" in list(marker.keys()): output_file.write("," + str(marker['additive'])) - if "dominance" in marker.keys(): + if "dominance" in list(marker.keys()): output_file.write("," + str(marker['dominance'])) if i < (len(markers) - 1): output_file.write("\n") def trim_markers_for_figure(markers): - if 'p_wald' in markers[0].keys(): + if 'p_wald' in list(markers[0].keys()): score_type = 'p_wald' - elif 'lod_score' in markers[0].keys(): + elif 'lod_score' in list(markers[0].keys()): score_type = 'lod_score' else: score_type = 'lrs_value' @@ -617,7 +617,7 @@ def trim_markers_for_figure(markers): return filtered_markers def trim_markers_for_table(markers): - if 'lod_score' in markers[0].keys(): + if 'lod_score' in list(markers[0].keys()): sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) else: sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) @@ -695,10 +695,10 @@ def get_genofile_samplelist(dataset): def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings = [] for sample in used_samples: - if sample in sample_list.sample_attribute_values.keys(): + if sample in list(sample_list.sample_attribute_values.keys()): combined_string = "" for var in categorical_vars: - if var in sample_list.sample_attribute_values[sample].keys(): + if var in list(sample_list.sample_attribute_values[sample].keys()): combined_string += str(sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" @@ -707,7 +707,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings.append(combined_string) - d = dict([(y,x+1) for x,y in enumerate(sorted(set(perm_strata_strings)))]) + d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))]) list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index f61c40b4..7916651f 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -23,7 +23,7 @@ from __future__ import absolute_import, print_function, division import sys import string -import cPickle +import pickle import os import time import pp @@ -202,8 +202,8 @@ class NetworkGraph(object): self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, - cols = range(len(self.traits)), - rows = range(len(self.traits)), + cols = list(range(len(self.traits))), + rows = list(range(len(self.traits))), samples = self.all_sample_list, sample_data = self.sample_data, elements = self.elements,) diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 8bc6b889..20319756 100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py @@ -1,7 +1,4 @@ from __future__ import absolute_import, print_function, division -import sys -reload(sys) -sys.setdefaultencoding('utf8') from flask import g class News(object): diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py index f7f61a09..917b9d31 100644 --- a/wqflask/wqflask/pbkdf2.py +++ b/wqflask/wqflask/pbkdf2.py @@ -44,7 +44,7 @@ import hmac import hashlib from struct import Struct from operator import xor -from itertools import izip, starmap +from itertools import starmap _pack_int = Struct('>I').pack @@ -66,13 +66,13 @@ def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None): def _pseudorandom(x, mac=mac): h = mac.copy() h.update(x) - return map(ord, h.digest()) + return list(map(ord, h.digest())) buf = [] - for block in xrange(1, -(-keylen // mac.digest_size) + 1): + for block in range(1, -(-keylen // mac.digest_size) + 1): rv = u = _pseudorandom(salt + _pack_int(block)) - for i in xrange(iterations - 1): + for i in range(iterations - 1): u = _pseudorandom(''.join(map(chr, u))) - rv = list(starmap(xor, izip(rv, u))) + rv = list(starmap(xor, zip(rv, u))) buf.extend(rv) return ''.join(map(chr, buf))[:keylen] @@ -81,7 +81,7 @@ def safe_str_cmp(a, b): if len(a) != len(b): return False rv = 0 - for x, y in izip(a, b): + for x, y in zip(a, b): rv |= ord(x) ^ ord(y) return rv == 0 @@ -92,14 +92,14 @@ def test(): def check(data, salt, iterations, keylen, expected): rv = pbkdf2_hex(data, salt, iterations, keylen) if rv != expected: - print 'Test failed:' - print ' Expected: %s' % expected - print ' Got: %s' % rv - print ' Parameters:' - print ' data=%s' % data - print ' salt=%s' % salt - print ' iterations=%d' % iterations - print + print('Test failed:') + print((' Expected: %s' % expected)) + print((' Got: %s' % rv)) + print(' Parameters:') + print((' data=%s' % data)) + print((' salt=%s' % salt)) + print((' iterations=%d' % iterations)) + print() failed.append(1) # From RFC 6070 diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 39a07310..6b3e00fb 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -125,7 +125,7 @@ def add_group_to_resource(): def get_group_names(group_masks): group_masks_with_names = {} - for group_id, group_mask in group_masks.iteritems(): + for group_id, group_mask in list(group_masks.items()): this_mask = group_mask group_name = get_group_info(group_id)['name'] this_mask['name'] = group_name diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index de4b01eb..c07a7670 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -53,7 +53,7 @@ views.py). search = self.search_terms self.original_search_string = self.search_terms # check for dodgy search terms - rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE) + rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE) if rx.match(search): logger.info("Regex failed search") self.search_term_exists = False @@ -266,7 +266,7 @@ def get_GO_symbols(a_search): def insert_newlines(string, every=64): """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """ lines = [] - for i in xrange(0, len(string), every): + for i in range(0, len(string), every): lines.append(string[i:i+every]) return '\n'.join(lines) diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index ad78ebcc..f17e825e 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -43,7 +43,7 @@ class SampleList(object): for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") - if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait + if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X': sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1])) else: @@ -57,7 +57,7 @@ class SampleList(object): sample = webqtlCaseData.webqtlCaseData(name=sample_name) sample.extra_info = {} - if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17'): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 253c887b..68c3ad7d 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -47,7 +47,7 @@ def get_export_metadata(trait_id, dataset_name): def dict_to_sorted_list(dictionary): - sorted_list = [item for item in dictionary.iteritems()] + sorted_list = [item for item in list(dictionary.items())] sorted_list = sorted(sorted_list, cmp=cmp_samples) sorted_values = [item[1] for item in sorted_list] return sorted_values diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index f188fd9d..738aa28a 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division import string import os import datetime -import cPickle +import pickle import uuid import requests import json as json @@ -261,7 +261,7 @@ class ShowTrait(object): hddn['export_data'] = "" hddn['export_format'] = "excel" if len(self.scales_in_geno) < 2: - hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0] + hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0] # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.hddn = hddn @@ -405,7 +405,7 @@ class ShowTrait(object): if not self.temp_trait: other_sample_names = [] - for sample in self.this_trait.data.keys(): + for sample in list(self.this_trait.data.keys()): if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names): primary_sample_names.append(self.this_trait.data[sample].name) primary_sample_names.remove(self.this_trait.data[sample].name2) @@ -558,7 +558,7 @@ def get_table_widths(sample_groups, has_num_cases=False): def has_num_cases(this_trait): has_n = False if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno": - for name, sample in this_trait.data.iteritems(): + for name, sample in list(this_trait.data.items()): if sample.num_cases: has_n = True break @@ -611,7 +611,7 @@ def get_categorical_variables(this_trait, sample_list): if len(sample_list.attributes) > 0: for attribute in sample_list.attributes: attribute_vals = [] - for sample_name in this_trait.data.keys(): + for sample_name in list(this_trait.data.keys()): if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes: attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name]) else: @@ -625,7 +625,7 @@ def get_categorical_variables(this_trait, sample_list): def get_genotype_scales(genofiles): geno_scales = {} - if type(genofiles) is list: + if isinstance(genofiles, list): for the_file in genofiles: file_location = the_file['location'] geno_scales[file_location] = get_scales_from_genofile(file_location) diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 1d28d76a..b18bfc62 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -459,7 +459,7 @@ class SnpBrowser(object): function_list = [] if function_details: function_list = string.split(string.strip(function_details), ",") - function_list = map(string.strip, function_list) + function_list = list(map(string.strip, function_list)) function_list[0] = function_list[0].title() function_details = ", ".join(item for item in function_list) function_details = function_details.replace("_", " ") @@ -725,11 +725,11 @@ def get_effect_details_by_category(effect_name = None, effect_value = None): codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] effect_detail_list = string.split(string.strip(effect_value), '|') - effect_detail_list = map(string.strip, effect_detail_list) + effect_detail_list = list(map(string.strip, effect_detail_list)) for index, item in enumerate(effect_detail_list): item_list = string.split(string.strip(item), ',') - item_list = map(string.strip, item_list) + item_list = list(map(string.strip, item_list)) gene_id = item_list[0] gene_name = item_list[1] diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index cfee0079..04672b45 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -193,7 +193,7 @@ def login(): if user_details: submitted_password = params['password'] pwfields = user_details['password'] - if type(pwfields) is str: + if isinstance(pwfields, str): pwfields = json.loads(pwfields) encrypted_pass_fields = encode_password(pwfields, submitted_password) password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password']) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index a871e91a..56d1c084 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -9,7 +9,7 @@ import uuid import hashlib import hmac import base64 -import urlparse +import urllib.parse import simplejson as json @@ -867,7 +867,7 @@ def forgot_password_submit(): email_address = params['email_address'] next_page = None if email_address != "": - logger.debug("Wants to send password E-mail to ",email_address) + logger.debug("Wants to send password E-mail to ", email_address) user_details = get_user_by_unique_column("email_address", email_address) if user_details: ForgotPasswordEmail(user_details["email_address"]) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index dde22bf7..83d5202e 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -14,13 +14,13 @@ import csv import simplejson as json import yaml import xlsxwriter -import StringIO # Todo: Use cStringIO? +import io # Todo: Use cStringIO? from zipfile import ZipFile, ZIP_DEFLATED import gc import numpy as np -import cPickle as pickle +import pickle as pickle import uuid import flask @@ -55,7 +55,7 @@ from wqflask.ctl import ctl_analysis from wqflask.snp_browser import snp_browser from utility import temp_data -from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH +from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH from utility.helper_functions import get_species_groups from utility.authentication_tools import check_resource_availability from utility.redis_tools import get_redis_conn @@ -133,10 +133,10 @@ def handle_bad_request(e): list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ] animation = random.choice(list) - resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation,version=GN_VERSION)) + resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION)) # logger.error("Set cookie %s with %s" % (err_msg, animation)) - resp.set_cookie(err_msg[:32],animation) + resp.set_cookie(err_msg[:32], animation) return resp @app.route("/authentication_needed") @@ -257,7 +257,7 @@ def docedit(): @app.route('/generated/<filename>') def generated_file(filename): logger.info(request.url) - return send_from_directory(GENERATED_IMAGE_DIR,filename) + return send_from_directory(GENERATED_IMAGE_DIR, filename) @app.route("/help") def help(): @@ -373,7 +373,7 @@ def export_trait_excel(): logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) - buff = StringIO.StringIO() + buff = io.StringIO() workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) worksheet = workbook.add_worksheet() for i, row in enumerate(sample_data): @@ -397,7 +397,7 @@ def export_trait_csv(): logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) - buff = StringIO.StringIO() + buff = io.StringIO() writer = csv.writer(buff) for row in sample_data: writer.writerow(row) @@ -417,7 +417,7 @@ def export_traits_csv(): file_list = export_traits.export_search_results_csv(request.form) if len(file_list) > 1: - memory_file = StringIO.StringIO() + memory_file = io.StringIO() with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf: for the_file in file_list: zf.writestr(the_file[0], the_file[1]) @@ -460,7 +460,7 @@ def export_perm_data(): ["#Comment: Results sorted from low to high peak linkage"] ] - buff = StringIO.StringIO() + buff = io.StringIO() writer = csv.writer(buff) writer.writerows(the_rows) for item in perm_info['perm_data']: @@ -533,7 +533,7 @@ def heatmap_page(): result = template_vars.__dict__ - for item in template_vars.__dict__.keys(): + for item in list(template_vars.__dict__.keys()): logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) @@ -637,7 +637,7 @@ def loading_page(): if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} - for key, value in initial_start_vars.iteritems(): + for key, value in list(initial_start_vars.items()): if key in wanted or key.startswith(('value:')): start_vars[key] = value @@ -737,7 +737,7 @@ def mapping_results_page(): 'transform' ) start_vars = {} - for key, value in initial_start_vars.iteritems(): + for key, value in list(initial_start_vars.items()): if key in wanted or key.startswith(('value:')): start_vars[key] = value #logger.debug("Mapping called with start_vars:", start_vars) @@ -943,5 +943,5 @@ def json_default_handler(obj): # logger.info("Not going to serialize Dataset") # return None else: - raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % ( - type(obj), repr(obj)) + raise TypeError('Object of type %s with value of %s is not JSON serializable' % ( + type(obj), repr(obj))) diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 880a1cb2..d79ad6df 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -60,7 +60,7 @@ class WGCNA(object): print("Starting WGCNA analysis on dataset") self.r_enableWGCNAThreads() # Enable multi threading self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] - print("Retrieved phenotype data from database", requestform['trait_list']) + print(("Retrieved phenotype data from database", requestform['trait_list'])) helper_functions.get_trait_db_obs(self, self.trait_db_list) self.input = {} # self.input contains the phenotype values we need to send to R @@ -101,13 +101,13 @@ class WGCNA(object): if requestform.get('SoftThresholds') is not None: powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")] rpow = r_unlist(r_c(powers)) - print "SoftThresholds: {} == {}".format(powers, rpow) + print(("SoftThresholds: {} == {}".format(powers, rpow))) self.sft = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5) - print "PowerEstimate: {}".format(self.sft[0]) + print(("PowerEstimate: {}".format(self.sft[0]))) self.results['PowerEstimate'] = self.sft[0] if self.sft[0][0] is ri.NA_Integer: - print "No power is suitable for the analysis, just use 1" + print("No power is suitable for the analysis, just use 1") self.results['Power'] = 1 # No power could be estimated else: self.results['Power'] = self.sft[0][0] # Use the estimated power @@ -122,7 +122,7 @@ class WGCNA(object): self.results['network'] = network # How many modules and how many gene per module ? - print "WGCNA found {} modules".format(r_table(network[1])) + print(("WGCNA found {} modules".format(r_table(network[1])))) self.results['nmod'] = r_length(r_table(network[1]))[0] # The iconic WCGNA plot of the modules in the hanging tree @@ -135,7 +135,7 @@ class WGCNA(object): sys.stdout.flush() def render_image(self, results): - print("pre-loading imgage results:", self.results['imgloc']) + print(("pre-loading imgage results:", self.results['imgloc'])) imgfile = open(self.results['imgloc'], 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") |