From beb6a9360ecc9edca19692e4081efc15292fb7d1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 08:28:44 +0000 Subject: [PATCH 018/100] Find external tools: refactored code to work with GNU Guix --- wqflask/utility/tools.py | 92 ++++++++++++++++++++++-------------------------- 1 file changed, 43 insertions(+), 49 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index b8a41f60..0db195df 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -9,76 +9,70 @@ import os import sys from wqflask import app -def get_setting(id,default,guess,get_valid_path): - """ - Resolve a setting from the environment or the global settings in app.config +def get_setting(id,default,guess,find_path): + """Resolve a setting from the environment or the global settings in + app.config, with get_valid_path is a function checking whether the + path points to an expected directory an returns the full path e.g. + + guess = os.environ.get('HOME')+'/pylmm' + get_setting('PYLMM_PATH',default,guess,get_valid_path) + + first tries the environment variable in +id+, next gets the Flask + app setting for the same +id+, next tries the path passed in with + +default+ and finally does an educated +guess+. + + In all, the environment overrides the others, next is the flask + setting, then the default and finally the guess (which is + $HOME/repo). A valid path is returned. If none is resolved an + exception is thrown. + + Note that we do not use the system path. This is on purpose + because it will mess up controlled (reproducible) deployment. The + proper way is to either use the GNU Guix defaults as listed in + etc/default_settings.py or override them yourself by creating a + different settings.py file (or setting the environment). + """ # ---- Check whether environment exists - path = get_valid_path(os.environ.get(id)) + path = find_path(os.environ.get(id)) # ---- Check whether setting exists setting = app.config.get(id) if not path: - path = get_valid_path(setting) + path = find_path(setting) # ---- Check whether default exists if not path: - path = get_valid_path(default) + path = find_path(default) # ---- Guess directory if not path: + guess = os.environ.get('HOME')+guess if not setting: setting = guess - path = get_valid_path(guess) + path = find_path(guess) if not path: - raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository') - + raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the path') return path -def pylmm_command(default=None): - """ - Return the path to the repository and the python command to call - """ - def get_valid_path(path): +def find_command(command,id1,default,guess): + def find_path(path): """Test for a valid repository""" if path: - sys.stderr.write("Trying PYLMM_PATH in "+path+"\n") - if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'): + sys.stderr.write("Trying "+id1+" in "+path+"\n") + binary = str.split(command)[0] + if path and os.path.isfile(path+'/'+binary): return path else: None - guess = os.environ.get('HOME')+'/pylmm_gn2' - path = get_setting('PYLMM_PATH',default,guess,get_valid_path) - pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py' - return path,pylmm_command - -def plink_command(default=None): - """ - Return the path to the repository and the python command to call - """ - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PLINK_PATH in "+path+"\n") - if path and os.path.isfile(path+'/plink'): - return path - else: - None + path = get_setting(id1,default,guess,find_path) + binary = path+'/'+command + sys.stderr.write("Found "+binary+"\n") + return path,binary - guess = os.environ.get('HOME')+'/plink_gemma' - path = get_setting('PLINK_PATH',default,guess,get_valid_path) - plink_command = path+'/plink' - return path,plink_command +def pylmm_command(default=None): + return find_command('pylmm_gn2/lmm.py',"PYLMM_PATH",default,'/pylmm2') def gemma_command(default=None): - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PLINK_PATH in "+path+"\n") - if path and os.path.isfile(path+'/plink'): - return path - else: - None + return find_command('gemma',"GEMMA_PATH",default,'/gemma') - guess = os.environ.get('HOME')+'/plink' - path = get_setting('PLINK_PATH',default,guess,get_valid_path) - gemma_command = path+'/gemma' - return path, gemma_command \ No newline at end of file +def plink_command(default=None): + return find_command('plink2',"PLINK_PATH",default,'/plink') -- cgit v1.2.3 From af7d0bca229f3ebaa80a16d1ce3a2bf1a8abd5df Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 08:37:55 +0000 Subject: [PATCH 023/100] WIP fixing all paths --- README.md | 2 + doc/GUIX-Reproducible-from-source.org | 14 +++- doc/README.org | 23 +++++- etc/default_settings.py | 15 ++-- wqflask/base/data_set.py | 3 +- wqflask/utility/tools.py | 82 ++++++++++------------ wqflask/wqflask/database.py | 5 +- .../wqflask/marker_regression/marker_regression.py | 6 +- wqflask/wqflask/show_trait/show_trait.py | 10 +-- 9 files changed, 94 insertions(+), 66 deletions(-) (limited to 'wqflask/utility') diff --git a/README.md b/README.md index 3d95d05f..db495910 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,8 @@ Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams, and colleagues. Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, Memphis TN, USA. +Join #genenetwork on irc.freenode.net. + Email labwilliams@gmail.com or rwilliams@uthsc.edu Older version available on SourceForge http://sourceforge.net/projects/genenetwork/ diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index 871156ed..4399ea26 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -4,6 +4,7 @@ - [[#introduction][Introduction]] - [[#binary-deployment][Binary deployment]] - [[#from-source-deployment][From source deployment]] + - [[#create-archive][Create archive]] * Introduction @@ -33,10 +34,21 @@ Once that is done we can add the guix-bioinformatics path with : env GUIX_PACKAGE_PATH=../guix-bioinformatics command -such as +So +#+begin_src sh :lang bash #+begin_src sh :lang bash gn-stable-guix$ env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork genenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2 genenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2 #+end_src sh :lang bash + +Install with + +#+begin_src sh :lang bash +gn-stable-guix$ env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2 +#+end_src sh :lang bash + +* Create archive + +: env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar diff --git a/doc/README.org b/doc/README.org index 375a5d20..d9730948 100644 --- a/doc/README.org +++ b/doc/README.org @@ -3,6 +3,7 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - [[#binary-deployment-wip][Binary deployment (WIP)]] + - [[#install-genenetwork-server][Install genenetwork server]] - [[#run-mysql-server][Run MySQL server]] - [[#start-the-gn2-server][Start the GN2 server]] - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]] @@ -16,7 +17,27 @@ explain the GeneNetwork deployment system which is based on GNU Guix * Binary deployment (WIP) GN can be deployed either as a binary tarball or as a GNU Guix -package. +package. First install GNU Guix following the instructions of the +[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html#Binary-Installation][binary installation]] using a tar ball from [[https://www.gnu.org/software/guix/download/][here]] and, update guix with a +'guix pull' and make guix visible in the path. More information +exists also in my [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org][guix-notes]]. + +With guix running you should be able to install python, for example. + +: guix package -i python2 + +This will make python appear in $HOME/.guix-profile/bin/python. Suggested +environment settings can be seen with + +: guix package --search-paths + +** Install genenetwork server + +Fetch the nar file and install it after adding the key with, for +example + +: cat signing-key.pub |.guix-profile/bin/guix archive --authorize +: guix archive --import < guix_gn2-2.0-9e9475053.nar ** Run MySQL server diff --git a/etc/default_settings.py b/etc/default_settings.py index 929bd687..48d3f66b 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -1,13 +1,14 @@ import os +import sys -LOGFILE = "/var/log/genenetwork/wqflask.log" +LOGFILE = "/tmp/genenetwork2.log" # This is needed because Flask turns key errors into a # 400 bad request response with no exception/log TRAP_BAD_REQUEST_ERRORS = True -DB_URI = "mysql://gn2:default@localhost/db_webqtl" -SQLALCHEMY_DATABASE_URI = 'mysql://gn2:default@localhost/db_webqtl' +DB_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" +SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' # http://pythonhosted.org/Flask-Security/configuration.html SECURITY_CONFIRMABLE = True @@ -22,7 +23,7 @@ SERVER_PORT = 5003 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' # Path overrides for Genenetwork -HOME=os.environ.get('HOME') -PYLMM_PATH = HOME+"/izip/git/opensource/python/pylmm_gn2/" -PLINK_PATH = HOME+"/.guix-profile/bin" -GEMMA_PATH = HOME+"/.guix-profile/bin" +GENENETWORK_FILES = "../../gn2_data" +PYLMM_RUN = os.popen("which pylmm_redis").read() +PLINK_RUN = os.popen("which plink2").read() +GEMMA_RUN = os.popen("which gemma").read() diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index e37a838f..0e5a3ac1 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -405,10 +405,11 @@ class DatasetGroup(object): #print("Cache not hit") from utility.tools import plink_command - PLINK_PATH,PLINK_COMMAND = plink_command() + PLINK_RUN = plink_command() geno_file_path = webqtlConfig.GENODIR+self.name+".geno" plink_file_path = PLINK_PATH+"/"+self.name+".fam" + # @FIXME PJOTR/ZACH: .fam files should go into FLATFILES if os.path.isfile(plink_file_path): self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 0db195df..c3c9b292 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -9,22 +9,22 @@ import os import sys from wqflask import app -def get_setting(id,default,guess,find_path): +def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with get_valid_path is a function checking whether the - path points to an expected directory an returns the full path e.g. + path points to an expected directory and returns the full path to + the binary command guess = os.environ.get('HOME')+'/pylmm' - get_setting('PYLMM_PATH',default,guess,get_valid_path) + get_setting('PYLMM_PATH',guess) first tries the environment variable in +id+, next gets the Flask - app setting for the same +id+, next tries the path passed in with - +default+ and finally does an educated +guess+. + app setting for the same +id+ and finally does an educated + +guess+. In all, the environment overrides the others, next is the flask - setting, then the default and finally the guess (which is - $HOME/repo). A valid path is returned. If none is resolved an - exception is thrown. + setting, then the guess. A valid path to the binary command is + returned. If none is resolved an exception is thrown. Note that we do not use the system path. This is on purpose because it will mess up controlled (reproducible) deployment. The @@ -33,46 +33,36 @@ def get_setting(id,default,guess,find_path): different settings.py file (or setting the environment). """ - # ---- Check whether environment exists - path = find_path(os.environ.get(id)) - # ---- Check whether setting exists - setting = app.config.get(id) - if not path: - path = find_path(setting) - # ---- Check whether default exists - if not path: - path = find_path(default) - # ---- Guess directory - if not path: - guess = os.environ.get('HOME')+guess - if not setting: - setting = guess - path = find_path(guess) - if not path: - raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the path') - return path - -def find_command(command,id1,default,guess): - def find_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying "+id1+" in "+path+"\n") - binary = str.split(command)[0] - if path and os.path.isfile(path+'/'+binary): - return path + def valid(command): + if command: + sys.stderr.write("Found value "+command+"\n") + return command else: - None + return None + + # ---- Check whether environment exists + sys.stderr.write("Looking for "+command_id+"\n") + command = valid(os.environ.get(command_id)) + if not command: + # ---- Check whether setting exists in app + command = valid(app.config.get(command_id)) + if not command: + command = valid(guess) + if not command: + raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path') + return command - path = get_setting(id1,default,guess,find_path) - binary = path+'/'+command - sys.stderr.write("Found "+binary+"\n") - return path,binary +def pylmm_command(guess=None): + return get_setting("PYLMM_RUN",guess) -def pylmm_command(default=None): - return find_command('pylmm_gn2/lmm.py',"PYLMM_PATH",default,'/pylmm2') +def gemma_command(guess=None): + return get_setting("GEMMA_RUN",guess) -def gemma_command(default=None): - return find_command('gemma',"GEMMA_PATH",default,'/gemma') +def plink_command(guess=None): + return get_setting("PLINK_RUN",guess) -def plink_command(default=None): - return find_command('plink2',"PLINK_PATH",default,'/plink') +def flat_files(subdir=None): + base = get_setting("GENENETWORK_FILES") + if subdir: + return base+"/"+subdir + return base diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index 159c5d6c..2f544d44 100755 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -24,8 +24,9 @@ def init_db(): # you will have to import them first before calling init_db() #import yourapplication.models import wqflask.model - print("Creating all..") + print("database.py: Creating all model metadata..") Base.metadata.create_all(bind=engine) - print("Done creating all...") + print("database.py: Done creating all model metadata...") + print("Point your browser at http://localhost:5003/") init_db() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index a657510d..b0f5ed69 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -46,9 +46,9 @@ from wqflask.marker_regression import gemma_mapping # runs at startup, so a missing binary will balk before running the # service -GEMMA_PATH,GEMMA_COMMAND = gemma_command() -PYLMM_PATH,PYLMM_COMMAND = pylmm_command() -PLINK_PATH,PLINK_COMMAND = plink_command() +GEMMA_RUN = gemma_command() +PYLMM_RUN = pylmm_command() +PLINK_RUN = plink_command() # RQTL_PATH,RQTL_COMMAND = rqtl_command() diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 2d4c952a..458e48da 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -16,7 +16,8 @@ from base import webqtlConfig from base import webqtlCaseData from wqflask.show_trait.SampleList import SampleList from utility import webqtlUtil, Plot, Bunch, helper_functions -from utility.tools import pylmm_command, plink_command +# from utility.tools import plink_command +from utility.tools import flat_files from base.trait import GeneralTrait from base import data_set from dbFunction import webqtlDatabaseFunction @@ -24,8 +25,7 @@ from basicStatistics import BasicStatisticsFunctions from pprint import pformat as pf -PYLMM_PATH,PYLMM_COMMAND = pylmm_command() -PLINK_PATH,PLINK_COMMAND = plink_command() +MAPPING_FILES = flat_files("mapping") ############################################### # @@ -162,8 +162,8 @@ class ShowTrait(object): def get_mapping_methods(self): '''Only display mapping methods when the dataset group's genotype file exists''' def check_plink_gemma(): - if (os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bed") and - os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".map")): + if (os.path.isfile(MAPPYING_FILES+"/"+self.dataset.group.name+".bed") and + os.path.isfile(MAPPING_FILES+"/"+self.dataset.group.name+".map")): return True else: return False -- cgit v1.2.3 From 4b80bbfe261e8d0587a637b35416834e027f0999 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 08:46:23 +0000 Subject: [PATCH 024/100] Sanitizing file handling --- wqflask/base/data_set.py | 29 ++++++++++------------------- wqflask/utility/tools.py | 20 +++++++++++++++----- wqflask/wqflask/show_trait/show_trait.py | 11 ++++------- 3 files changed, 29 insertions(+), 31 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 0e5a3ac1..c6f34143 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,12 +44,15 @@ from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks +from utility.tools import flat_files from maintenance import get_group_samplelists from MySQLdb import escape_string as escape from pprint import pformat as pf +MAPPING_PATH = flat_files("mapping") + # Used by create_database to instantiate objects # Each subclass will add to this DS_NAME_MAP = {} @@ -404,15 +407,11 @@ class DatasetGroup(object): else: #print("Cache not hit") - from utility.tools import plink_command - PLINK_RUN = plink_command() - geno_file_path = webqtlConfig.GENODIR+self.name+".geno" - plink_file_path = PLINK_PATH+"/"+self.name+".fam" - # @FIXME PJOTR/ZACH: .fam files should go into FLATFILES - if os.path.isfile(plink_file_path): - self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path) + mapping_file_path = MAPPING_PATH+"/"+self.name+".fam" + if os.path.isfile(mapping_file_path): + self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_file_path) elif os.path.isfile(geno_file_path): self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path) else: @@ -441,18 +440,10 @@ class DatasetGroup(object): # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - if os.path.isfile(full_filename): - #print("Reading file: ", full_filename) - genotype_1.read(full_filename) - #print("File read") - else: - try: - full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno')) - #print("Reading file") - genotype_1.read(full_filename) - #print("File read") - except IOError: - print("File doesn't exist!") + if not os.path.isfile(full_filename): + raise SystemError("File "+full_filename+" does not exist") + print("Reading file: ", full_filename) + genotype_1.read(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index c3c9b292..44bbb1b0 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -52,17 +52,27 @@ def get_setting(command_id,guess=None): raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path') return command +def valid_bin(bin): + if os.path.islink(bin) or os.path.isfile(bin): + return bin + return None + +def valid_path(dir): + if os.path.isdir(dir): + return dir + return None + def pylmm_command(guess=None): - return get_setting("PYLMM_RUN",guess) + return valid_bin(get_setting("PYLMM_RUN",guess)) def gemma_command(guess=None): - return get_setting("GEMMA_RUN",guess) + return valid_bin(get_setting("GEMMA_RUN",guess)) def plink_command(guess=None): - return get_setting("PLINK_RUN",guess) + return valid_bin(get_setting("PLINK_RUN",guess)) def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: - return base+"/"+subdir - return base + return valid_path(base+"/"+subdir) + return valid_path(base) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 458e48da..35f7fe5f 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -16,8 +16,6 @@ from base import webqtlConfig from base import webqtlCaseData from wqflask.show_trait.SampleList import SampleList from utility import webqtlUtil, Plot, Bunch, helper_functions -# from utility.tools import plink_command -from utility.tools import flat_files from base.trait import GeneralTrait from base import data_set from dbFunction import webqtlDatabaseFunction @@ -25,7 +23,8 @@ from basicStatistics import BasicStatisticsFunctions from pprint import pformat as pf -MAPPING_FILES = flat_files("mapping") +from utility.tools import flat_files +MAPPING_PATH = flat_files("mapping") ############################################### # @@ -34,8 +33,6 @@ MAPPING_FILES = flat_files("mapping") # ############################################## - - class ShowTrait(object): def __init__(self, kw): @@ -162,8 +159,8 @@ class ShowTrait(object): def get_mapping_methods(self): '''Only display mapping methods when the dataset group's genotype file exists''' def check_plink_gemma(): - if (os.path.isfile(MAPPYING_FILES+"/"+self.dataset.group.name+".bed") and - os.path.isfile(MAPPING_FILES+"/"+self.dataset.group.name+".map")): + if (os.path.isfile(MAPPYING_PATH+"/"+self.dataset.group.name+".bed") and + os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".map")): return True else: return False -- cgit v1.2.3 From 94e3ac8e2fff5da72fd1c0358fdb6fdad9a7830c Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 22 Feb 2016 16:26:13 +0000 Subject: Introducing TEMPDIR --- wqflask/utility/tools.py | 14 ++++++++++---- wqflask/wqflask/views.py | 3 ++- 2 files changed, 12 insertions(+), 5 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 44bbb1b0..dc7bc33c 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -9,6 +9,7 @@ import os import sys from wqflask import app + def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with get_valid_path is a function checking whether the @@ -33,7 +34,7 @@ def get_setting(command_id,guess=None): different settings.py file (or setting the environment). """ - def valid(command): + def value(command): if command: sys.stderr.write("Found value "+command+"\n") return command @@ -42,12 +43,12 @@ def get_setting(command_id,guess=None): # ---- Check whether environment exists sys.stderr.write("Looking for "+command_id+"\n") - command = valid(os.environ.get(command_id)) + command = value(os.environ.get(command_id)) if not command: # ---- Check whether setting exists in app - command = valid(app.config.get(command_id)) + command = value(app.config.get(command_id)) if not command: - command = valid(guess) + command = value(guess) if not command: raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path') return command @@ -76,3 +77,8 @@ def flat_files(subdir=None): if subdir: return valid_path(base+"/"+subdir) return valid_path(base) + +def tempdir(): + return valid_path(get_setting("TEMPDIR","/tmp")) + +TEMPDIR = tempdir() diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3bf64a18..929da649 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -50,6 +50,7 @@ from wqflask.correlation import corr_scatter_plot from wqflask.wgcna import wgcna_analysis from utility import temp_data +from utility.tools import TEMPDIR from base import webqtlFormData from utility.benchmark import Bench @@ -423,7 +424,7 @@ def marker_regression_page(): print("img_path:", img_path) initial_start_vars = request.form print("initial_start_vars:", initial_start_vars) - imgfile = open('/home/zas1024/tmp/' + img_path, 'rb') + imgfile = open(TEMPDIR + '/' + img_path, 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") bytesarray = array.array('B', imgB64) -- cgit v1.2.3 From 3be9e4a0950b1ea2d560463032c6f4104baf738e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 08:49:59 +0000 Subject: [PATCH 026/100] Introducing cached values PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR --- wqflask/utility/tools.py | 8 +++++++- wqflask/wqflask/marker_regression/marker_regression.py | 11 +---------- 2 files changed, 8 insertions(+), 11 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index dc7bc33c..5d69e699 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -81,4 +81,10 @@ def flat_files(subdir=None): def tempdir(): return valid_path(get_setting("TEMPDIR","/tmp")) -TEMPDIR = tempdir() +# Cached values + +PYLMM_COMMAND = pylmm_command() +GEMMA_COMMAND = pylmm_command() +PLINK_COMMAND = pylmm_command() +FLAT_FILES = flat_files() +TEMPDIR = tempdir() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index b0f5ed69..a76a5967 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -36,21 +36,12 @@ from utility import helper_functions from utility import Plot, Bunch from utility import temp_data from utility.benchmark import Bench -from utility.tools import pylmm_command, plink_command, gemma_command from wqflask.marker_regression import gemma_mapping #from wqflask.marker_regression import qtl_reaper_mapping #from wqflask.marker_regression import plink_mapping #from wqflask.marker_regression import rqtl_mapping -# Check for valid binary paths of pylmm, plink, rqtl etc. This code -# runs at startup, so a missing binary will balk before running the -# service - -GEMMA_RUN = gemma_command() -PYLMM_RUN = pylmm_command() -PLINK_RUN = plink_command() -# RQTL_PATH,RQTL_COMMAND = rqtl_command() - +from utility.tools import PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND class MarkerRegression(object): -- cgit v1.2.3 From 1675f34eeff84d7ec0f43c1676f9107e202dda88 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 08:51:57 +0000 Subject: [PATCH 027/100] Introduce tools.locate --- wqflask/utility/tools.py | 14 +++++++++++++- wqflask/wqflask/marker_regression/marker_regression.py | 5 ++--- 2 files changed, 15 insertions(+), 4 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 5d69e699..624df179 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -78,11 +78,23 @@ def flat_files(subdir=None): return valid_path(base+"/"+subdir) return valid_path(base) +def locate(name, subdir=None): + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_path(lookfor): + return lookfor + else: + raise IOError("Can not locate "+lookfor) + raise IOError("Can not locate "+name) + def tempdir(): return valid_path(get_setting("TEMPDIR","/tmp")) + # Cached values - PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = pylmm_command() PLINK_COMMAND = pylmm_command() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index a76a5967..36334317 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -41,7 +41,7 @@ from wqflask.marker_regression import gemma_mapping #from wqflask.marker_regression import plink_mapping #from wqflask.marker_regression import rqtl_mapping -from utility.tools import PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND +from utility.tools import locate, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND class MarkerRegression(object): @@ -979,8 +979,7 @@ class MarkerRegression(object): #def gen_human_results(self, pheno_vector, tempdata): def gen_human_results(self, pheno_vector, key, temp_uuid): - file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name) - print("file_base:", file_base) + file_base = locate(self.dataset.group.name,"mapping") plink_input = input.plink(file_base, type='b') input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz") -- cgit v1.2.3 From ae8834ac9c0f15f2c397bb6727b8a8079bf175eb Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 23 Feb 2016 07:46:43 +0000 Subject: tools.py: add function locate_without_error --- wqflask/utility/tools.py | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 624df179..af1ab353 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -79,6 +79,11 @@ def flat_files(subdir=None): return valid_path(base) def locate(name, subdir=None): + """ + Locate a static flat file in the GENENETWORK_FILES environment. + + This function throws an error when the file is not found. + """ base = get_setting("GENENETWORK_FILES") if subdir: base = base+"/"+subdir @@ -89,7 +94,24 @@ def locate(name, subdir=None): else: raise IOError("Can not locate "+lookfor) raise IOError("Can not locate "+name) - + +def locate_without_error(name, subdir=None): + """ + Locate a static flat file in the GENENETWORK_FILES environment. + + This function does not throw an error when the file is not found + but returns None. + """ + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_path(lookfor): + return lookfor + sys.stderr.write("WARNING: file "+name+" not found\n") + return None + def tempdir(): return valid_path(get_setting("TEMPDIR","/tmp")) -- cgit v1.2.3 From 6c0f35e56e8d26a47d210b12c171bb050d1ab150 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 23 Feb 2016 09:27:57 +0000 Subject: Fine tuning file locating --- wqflask/utility/tools.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index af1ab353..dd40be99 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -54,10 +54,15 @@ def get_setting(command_id,guess=None): return command def valid_bin(bin): - if os.path.islink(bin) or os.path.isfile(bin): + if os.path.islink(bin) or valid_file(bin): return bin return None +def valid_file(fn): + if os.path.isfile(fn): + return fn + return None + def valid_path(dir): if os.path.isdir(dir): return dir @@ -89,11 +94,12 @@ def locate(name, subdir=None): base = base+"/"+subdir if valid_path(base): lookfor = base + "/" + name - if valid_path(lookfor): + if valid_file(lookfor): return lookfor else: raise IOError("Can not locate "+lookfor) - raise IOError("Can not locate "+name) + if subdir: sys.stderr.write(subdir) + raise IOError("Can not locate "+name+" in "+base) def locate_without_error(name, subdir=None): """ @@ -107,7 +113,7 @@ def locate_without_error(name, subdir=None): base = base+"/"+subdir if valid_path(base): lookfor = base + "/" + name - if valid_path(lookfor): + if valid_file(lookfor): return lookfor sys.stderr.write("WARNING: file "+name+" not found\n") return None -- cgit v1.2.3 From 218fd0c7666583748098f0b7b4286b6d1cbf6838 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 23 Feb 2016 11:16:33 +0000 Subject: [PATCH 033/100] Refactored file searching --- wqflask/base/data_set.py | 16 ++++++++-------- wqflask/utility/tools.py | 4 +++- 2 files changed, 11 insertions(+), 9 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9ffc09ac..ce13dd77 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import locate +from utility.tools import locate, locate_without_error from maintenance import get_group_samplelists @@ -405,15 +405,15 @@ class DatasetGroup(object): else: print("Cache not hit") - geno_file_path = locate(self.name+".geno",'genotype') - mapping_file_path = locate(self.name+".fam",'mapping') - if os.path.isfile(mapping_file_path): - self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_file_path) - elif os.path.isfile(geno_file_path): - self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path) + genotype_fn = locate_without_error(self.name+".geno",'genotype') + mapping_fn = locate_without_error(self.name+".fam",'mapping') + if mapping_fn: + self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn) + elif genotype_fn: + self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) else: self.samplelist = None - #print("after get_samplelist") + print("Sample list: ",self.samplelist) Redis.set(key, json.dumps(self.samplelist)) Redis.expire(key, 60*5) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index dd40be99..d4c10c68 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -36,7 +36,7 @@ def get_setting(command_id,guess=None): """ def value(command): if command: - sys.stderr.write("Found value "+command+"\n") + sys.stderr.write("Found path "+command+"\n") return command else: return None @@ -95,6 +95,7 @@ def locate(name, subdir=None): if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): + print("Found: file "+lookfor+"\n") return lookfor else: raise IOError("Can not locate "+lookfor) @@ -114,6 +115,7 @@ def locate_without_error(name, subdir=None): if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): + print("Found: file "+name+"\n") return lookfor sys.stderr.write("WARNING: file "+name+" not found\n") return None -- cgit v1.2.3 From 92fda7557645199276bf4f8a65c40252c4d83c21 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Wed, 24 Feb 2016 09:25:43 +0000 Subject: Settled on the _COMMAND syntax over _RUN --- etc/default_settings.py | 6 +++--- wqflask/utility/tools.py | 10 +++------- 2 files changed, 6 insertions(+), 10 deletions(-) (limited to 'wqflask/utility') diff --git a/etc/default_settings.py b/etc/default_settings.py index 48d3f66b..6a218f26 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -24,6 +24,6 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a # Path overrides for Genenetwork GENENETWORK_FILES = "../../gn2_data" -PYLMM_RUN = os.popen("which pylmm_redis").read() -PLINK_RUN = os.popen("which plink2").read() -GEMMA_RUN = os.popen("which gemma").read() +PYLMM_COMMAND = os.popen("which pylmm_redis").read() +PLINK_COMMAND = os.popen("which plink2").read() +GEMMA_COMMAND = os.popen("which gemma").read() diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index d4c10c68..0f2e4d88 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -1,9 +1,5 @@ # Tools/paths finder resolves external paths from settings and/or environment # variables -# -# Currently supported: -# -# PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool import os import sys @@ -69,13 +65,13 @@ def valid_path(dir): return None def pylmm_command(guess=None): - return valid_bin(get_setting("PYLMM_RUN",guess)) + return valid_bin(get_setting("PYLMM_COMMAND",guess)) def gemma_command(guess=None): - return valid_bin(get_setting("GEMMA_RUN",guess)) + return valid_bin(get_setting("GEMMA_COMMAND",guess)) def plink_command(guess=None): - return valid_bin(get_setting("PLINK_RUN",guess)) + return valid_bin(get_setting("PLINK_COMMAND",guess)) def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") -- cgit v1.2.3 From 5fffa1aa4260af6663c1f9b4cf7494d3ebc6995d Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 24 Feb 2016 11:01:29 +0000 Subject: [PATCH 037/100] WebQtlConfig: sanitizing naming and used vars --- bin/genenetwork2 | 2 +- wqflask/base/data_set.py | 194 ++++++++++----------- wqflask/base/webqtlFormData.py | 2 +- .../basicStatistics/BasicStatisticsFunctions.py | 6 +- wqflask/maintenance/get_group_samplelists.py | 3 +- wqflask/utility/tools.py | 11 +- wqflask/wqflask/correlation/show_corr_results.py | 2 +- .../wqflask/correlation_matrix/show_corr_matrix.py | 1 - wqflask/wqflask/heatmap/heatmap.py | 2 - .../interval_analyst/IntervalAnalystPage.py | 138 +++++++-------- .../marker_regression/MarkerRegressionPage.py | 6 +- .../wqflask/marker_regression/marker_regression.py | 2 +- .../marker_regression/marker_regression_gn1.py | 116 ++++++------ wqflask/wqflask/search_results.py | 1 - wqflask/wqflask/show_trait/show_trait.py | 2 +- 15 files changed, 246 insertions(+), 242 deletions(-) (limited to 'wqflask/utility') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 54eee02e..00ee09bf 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,6 +1,6 @@ #! /bin/bash # -# This will run the server with default settings +# This will run the server with default settings. # Absolute path to this script, e.g. /home/user/bin/foo.sh SCRIPT=$(readlink -f "$0") diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index ce13dd77..6527657a 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -76,22 +76,22 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): #def get_dataset_type_from_json(dataset_name): - + class Dataset_Types(object): - + def __init__(self): self.datasets = {} file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) - + print("*" * 70) for species in data['datasets']: for group in data['datasets'][species]: for dataset_type in data['datasets'][species][group]: for dataset in data['datasets'][species][group][dataset_type]: #print("dataset is:", dataset) - + short_dataset_name = dataset[1] if dataset_type == "Phenotypes": new_type = "Publish" @@ -100,32 +100,32 @@ class Dataset_Types(object): else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type - + def __call__(self, name): return self.datasets[name] - + # Do the intensive work at startup one time only Dataset_Getter = Dataset_Types() # #print("Running at startup:", get_dataset_type_from_json("HBTRC-MLPFC_0611")) - + def create_datasets_list(): key = "all_datasets" result = Redis.get(key) - + if result: print("Cache hit!!!") datasets = pickle.loads(result) - + else: datasets = list() with Bench("Creating DataSets object"): type_dict = {'Publish': 'PublishFreeze', 'ProbeSet': 'ProbeSetFreeze', 'Geno': 'GenoFreeze'} - + for dataset_type in type_dict: query = "SELECT Name FROM {}".format(type_dict[dataset_type]) for result in g.db.execute(query).fetchall(): @@ -134,10 +134,10 @@ def create_datasets_list(): #print("type: {}\tname: {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) - + Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) - + return datasets @@ -158,30 +158,30 @@ def mescape(*items): class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): - json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json')) + json_data_fh = open(locate(name + '.json','genotype/json')) try: markers = json.load(json_data_fh) except: markers = [] - + for marker in markers: if (marker['chr'] != "X") and (marker['chr'] != "Y"): marker['chr'] = int(marker['chr']) marker['Mb'] = float(marker['Mb']) - + self.markers = markers #print("self.markers:", self.markers) - - + + def add_pvalues(self, p_values): print("length of self.markers:", len(self.markers)) print("length of p_values:", len(p_values)) - + if type(p_values) is 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): if not p_value: continue @@ -214,7 +214,7 @@ class Markers(object): #self.markers.remove(marker) #del self.markers[i] self.markers = filtered_markers - + #for i, marker in enumerate(self.markers): # if not 'p_value' in marker: @@ -223,9 +223,9 @@ class Markers(object): # #self.markers.remove(self.markers[i]) class HumanMarkers(Markers): - + def __init__(self, name, specified_markers = []): - marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + name + '.bim')) + marker_data_fh = open(locate('genotype') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() @@ -244,7 +244,7 @@ class HumanMarkers(Markers): marker['name'] = splat[1] marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) - + #print("markers is: ", pf(self.markers)) @@ -257,26 +257,26 @@ class HumanMarkers(Markers): # 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 - + #print("p_values2:", pf(p_values)) super(HumanMarkers, self).add_pvalues(p_values) - + #with Bench("deleting markers"): # markers = [] # for marker in self.markers: # if not marker['Mb'] <= 0 and not marker['chr'] == 0: # markers.append(marker) # self.markers = markers - - + + class DatasetGroup(object): """ Each group has multiple datasets; each species has multiple groups. - + For example, Mouse has multiple groups (BXD, BXA, etc), and each group has multiple datasets associated with it. - + """ def __init__(self, dataset): """This sets self.group and self.group_id""" @@ -284,14 +284,14 @@ class DatasetGroup(object): self.name, self.id = g.db.execute(dataset.query_for_group).fetchone() if self.name == 'BXD300': self.name = "BXD" - + self.f1list = None self.parlist = None self.get_f1_parent_strains() #print("parents/f1s: {}:{}".format(self.parlist, self.f1list)) - + self.species = webqtlDatabaseFunction.retrieve_species(self.name) - + self.incparentsf1 = False self.allsamples = None self._datasets = None @@ -302,7 +302,7 @@ class DatasetGroup(object): def get_markers(self): #print("self.species is:", self.species) if self.species == "human": - marker_class = HumanMarkers + marker_class = HumanMarkers else: marker_class = Markers @@ -356,7 +356,7 @@ class DatasetGroup(object): dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) else: dataset_sub_menu = [item[1:] for item in dataset] - + tissue_already_exists = False tissue_position = None for i, tissue_dict in enumerate(dataset_menu): @@ -384,7 +384,7 @@ class DatasetGroup(object): f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name] except KeyError: f1 = f12 = maternal = paternal = None - + if f1 and f12: self.f1list = [f1, f12] if maternal and paternal: @@ -455,18 +455,18 @@ class DatasetGroup(object): #self.samplelist = list(self.genotype.prgy) self.samplelist = list(genotype.prgy) - + return genotype #class DataSets(object): # """Builds a list of DataSets""" -# +# # def __init__(self): # self.datasets = list() -# +# + - #query = """SELECT Name FROM ProbeSetFreeze # UNION # SELECT Name From PublishFreeze @@ -501,7 +501,7 @@ class DataSet(object): self.check_confidentiality() self.retrieve_other_names() - + self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype if get_samplelist == True: self.group.get_samplelist() @@ -511,30 +511,30 @@ class DataSet(object): def get_desc(self): """Gets overridden later, at least for Temp...used by trait's get_given_name""" return None - + #@staticmethod #def get_by_trait_id(trait_id): # """Gets the dataset object given the trait id""" - # - # # - # name = g.db.execute(""" SELECT - # + # + # + # name = g.db.execute(""" SELECT + # # """) - # + # # return DataSet(name) # Delete this eventually @property def riset(): Weve_Renamed_This_As_Group - - + + #@property #def group(self): # if not self._group: # self.get_group() - # + # # return self._group @@ -546,7 +546,7 @@ class DataSet(object): This is not meant to retrieve the data set info if no name at all is passed. """ - + try: if self.type == "ProbeSet": query_args = tuple(escape(x) for x in ( @@ -582,17 +582,17 @@ class DataSet(object): except TypeError: print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - + def get_trait_data(self, sample_list=None): if sample_list: self.samplelist = sample_list else: self.samplelist = self.group.samplelist - + if self.group.parlist != None and self.group.f1list != None: if (self.group.parlist + self.group.f1list) in self.samplelist: self.samplelist += self.group.parlist + self.group.f1list - + query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species WHERE Strain.Name IN {} @@ -610,9 +610,9 @@ class DataSet(object): trait_sample_data = [] for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): - #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId + #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId #tempTable = None - #if GeneId and db.type == "ProbeSet": + #if GeneId and db.type == "ProbeSet": # if method == "3": # tempTable = self.getTempLiteratureTable(species=species, # input_species_geneid=GeneId, @@ -623,7 +623,7 @@ class DataSet(object): # TissueProbeSetFreezeId=tissueProbeSetFreezeId, # method=method, # returnNumber=returnNumber) - + if self.type == "Publish": dataset_type = "Phenotype" else: @@ -644,7 +644,7 @@ class DataSet(object): left join {}Data as T{} on T{}.Id = {}XRef.DataId and T{}.StrainId={}\n """.format(*mescape(self.type, item, item, self.type, item, item)) - + if self.type == "Publish": query += """ WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId @@ -661,16 +661,16 @@ class DataSet(object): order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.type, self.name, dataset_type, self.type, self.type, dataset_type)) - + #print("trait data query: ", query) - + results = g.db.execute(query).fetchall() #print("query results:", results) trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) self.trait_data = collections.defaultdict(list) - + # put all of the separate data together into a dictionary where the keys are # trait names and values are lists of sample values for trait_counter in range(trait_count): @@ -683,9 +683,9 @@ class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): - + #print("IS A PHENOTYPEDATASET") - + # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', @@ -756,26 +756,26 @@ class PhenotypeDataSet(DataSet): def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: - + if not this_trait.haveinfo: this_trait.retrieve_info(get_qtl_info=True) description = this_trait.post_publication_description - + #If the dataset is confidential and the user has access to confidential #phenotype traits, then display the pre-publication description instead #of the post-publication description if this_trait.confidential: this_trait.description_display = "" continue # for now - + if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): - + description = this_trait.pre_publication_description - + if len(description) > 0: this_trait.description_display = description.strip() else: @@ -820,7 +820,7 @@ class PhenotypeDataSet(DataSet): this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb)) - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -878,7 +878,7 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - + def get_trait_list(self): query = """ select Geno.Name @@ -912,7 +912,7 @@ class GenotypeDataSet(DataSet): this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) this_trait.location_value = trait_location_value - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -1004,7 +1004,7 @@ class MrnaAssayDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - + def get_trait_list_1(self): query = """ select ProbeSet.Name @@ -1020,7 +1020,7 @@ class MrnaAssayDataSet(DataSet): trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) #print("After retrieve_sample_data") return trait_data - + #def get_trait_data(self): # self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list # query = """ @@ -1040,9 +1040,9 @@ class MrnaAssayDataSet(DataSet): # trait_sample_data = [] # for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): # - # #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId + # #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId # #tempTable = None - # #if GeneId and db.type == "ProbeSet": + # #if GeneId and db.type == "ProbeSet": # # if method == "3": # # tempTable = self.getTempLiteratureTable(species=species, # # input_species_geneid=GeneId, @@ -1053,7 +1053,7 @@ class MrnaAssayDataSet(DataSet): # # TissueProbeSetFreezeId=tissueProbeSetFreezeId, # # method=method, # # returnNumber=returnNumber) - # + # # temp = ['T%s.value' % item for item in sample_ids_step] # query = "SELECT {}.Name,".format(escape(self.type)) # data_start_pos = 1 @@ -1067,7 +1067,7 @@ class MrnaAssayDataSet(DataSet): # left join {}Data as T{} on T{}.Id = {}XRef.DataId # and T{}.StrainId={}\n # """.format(*mescape(self.type, item, item, self.type, item, item)) - # + # # query += """ # WHERE {}XRef.{}FreezeId = {}Freeze.Id # and {}Freeze.Name = '{}' @@ -1080,7 +1080,7 @@ class MrnaAssayDataSet(DataSet): # # trait_count = len(trait_sample_data[0]) # self.trait_data = collections.defaultdict(list) - # + # # # put all of the separate data together into a dictionary where the keys are # # trait names and values are lists of sample values # for trait_counter in range(trait_count): @@ -1088,11 +1088,11 @@ class MrnaAssayDataSet(DataSet): # for chunk_counter in range(int(number_chunks)): # self.trait_data[trait_name] += ( # trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) - + def get_trait_info(self, trait_list=None, species=''): - # Note: setting trait_list to [] is probably not a great idea. + # Note: setting trait_list to [] is probably not a great idea. if not trait_list: trait_list = [] @@ -1155,7 +1155,7 @@ class MrnaAssayDataSet(DataSet): #print("query is:", pf(query)) result = g.db.execute(query).fetchone() - + mean = result[0] if result else 0 if mean: @@ -1176,7 +1176,7 @@ class MrnaAssayDataSet(DataSet): Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) result = g.db.execute(query).fetchone() - + if result: #if result[0] and result[1]: # lrs_chr = result[0] @@ -1184,7 +1184,7 @@ class MrnaAssayDataSet(DataSet): lrs_chr, lrs_mb = result #XZ: LRS_location_value is used for sorting lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb) - + #try: # lrs_location_value = int(lrs_chr)*1000 + float(lrs_mb) #except: @@ -1197,7 +1197,7 @@ class MrnaAssayDataSet(DataSet): this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb)) - + def convert_location_to_value(self, chromosome, mb): try: @@ -1208,7 +1208,7 @@ class MrnaAssayDataSet(DataSet): else: location_value = (ord(str(chromosome).upper()[0])*1000 + float(mb)) - + return location_value def get_sequence(self): @@ -1225,7 +1225,7 @@ class MrnaAssayDataSet(DataSet): """ % (escape(self.name), escape(self.dataset.name)) results = g.db.execute(query).fetchone() return results[0] - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -1246,8 +1246,8 @@ class MrnaAssayDataSet(DataSet): results = g.db.execute(query).fetchall() #print("RETRIEVED RESULTS HERE:", results) return results - - + + def retrieve_genes(self, column_name): query = """ select ProbeSet.Name, ProbeSet.%s @@ -1256,7 +1256,7 @@ class MrnaAssayDataSet(DataSet): ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) results = g.db.execute(query).fetchall() - + return dict(results) #def retrieve_gene_symbols(self): @@ -1285,8 +1285,8 @@ class MrnaAssayDataSet(DataSet): # for item in results: # symbol_dict[item[0]] = item[1] # return symbol_dict - - + + class TempDataSet(DataSet): @@ -1308,8 +1308,8 @@ class TempDataSet(DataSet): self.id = 1 self.fullname = 'Temporary Storage' self.shortname = 'Temp' - - + + @staticmethod def handle_pca(desc): if 'PCA' in desc: @@ -1318,13 +1318,13 @@ class TempDataSet(DataSet): else: desc = desc[:desc.index('entered')].strip() return desc - + def get_desc(self): g.db.execute('SELECT description FROM Temp WHERE Name=%s', self.name) desc = g.db.fetchone()[0] desc = self.handle_pca(desc) - return desc - + return desc + def get_group(self): self.cursor.execute(""" SELECT @@ -1337,7 +1337,7 @@ class TempDataSet(DataSet): """, self.name) self.group, self.group_id = self.cursor.fetchone() #return self.group - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -1351,7 +1351,7 @@ class TempDataSet(DataSet): Order BY Strain.Name """ % escape(trait.name) - + results = g.db.execute(query).fetchall() diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 44fdcc3f..10251756 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -157,7 +157,7 @@ class webqtlFormData(object): self.genotype_1 = reaper.Dataset() - full_filename = os.path.join(webqtlConfig.GENODIR, self.group + '.geno') + full_filename = locate(self.group + '.geno','genotype') # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(full_filename) diff --git a/wqflask/basicStatistics/BasicStatisticsFunctions.py b/wqflask/basicStatistics/BasicStatisticsFunctions.py index 74784853..e748a822 100755 --- a/wqflask/basicStatistics/BasicStatisticsFunctions.py +++ b/wqflask/basicStatistics/BasicStatisticsFunctions.py @@ -118,7 +118,7 @@ def plotNormalProbability(vals=None, RISet='', title=None, showstrains=0, specia Plot.plotXY(c, dataZ, dataX, dataLabel = dataLabel, XLabel='Expected Z score', connectdot=0, YLabel='Trait value', title=title, specialCases=specialStrains, showLabel = showLabel) filename= webqtlUtil.genRandStr("nP_") - c.save(webqtlConfig.IMGDIR+filename, format='gif') + c.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif') img=HT.Image('/image/'+filename+'.gif',border=0) @@ -145,7 +145,7 @@ def plotBoxPlot(vals): Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") filename= webqtlUtil.genRandStr("Box_") - canvas.save(webqtlConfig.IMGDIR+filename, format='gif') + canvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif') img=HT.Image('/image/'+filename+'.gif',border=0) plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13")) @@ -201,7 +201,7 @@ def plotBarGraph(identification='', RISet='', vals=None, type="name"): Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title=title, sLabel = sLabel, barSpace = sw) filename= webqtlUtil.genRandStr("Bar_") - c.save(webqtlConfig.IMGDIR+filename, format='gif') + c.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif') img=HT.Image('/image/'+filename+'.gif',border=0) return img diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index b8397b47..a9059fad 100755 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -6,7 +6,6 @@ import gzip from base import webqtlConfig - def process_genofiles(geno_dir=webqtlConfig.GENODIR): print("Yabba") #sys.exit("Dabba") @@ -54,4 +53,4 @@ def get_samplelist_from_plink(genofilename): line = line.split(" ") samplelist.append(line[0]) - return samplelist \ No newline at end of file + return samplelist diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 0f2e4d88..c0f6a49a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -79,6 +79,15 @@ def flat_files(subdir=None): return valid_path(base+"/"+subdir) return valid_path(base) +def assert_dir(dir): + if not valid_path(dir): + raise Exception("ERROR: can not find directory "+dir) + return dir + +def mk_dir(dir): + os.makedirs(dir) + return assert_dir(dir) + def locate(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -98,7 +107,7 @@ def locate(name, subdir=None): if subdir: sys.stderr.write(subdir) raise IOError("Can not locate "+name+" in "+base) -def locate_without_error(name, subdir=None): +def locate_ignore_error(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 21a2c26c..06b4860e 100755 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -943,7 +943,7 @@ class CorrelationResults(object): use_tissue_corr = True DatabaseFileName = self.getFileName( target_db_name=self.target_db_name ) - datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r') + datasetFile = open(webqtlConfig.CACHEDIR+DatabaseFileName,'r') #XZ, 01/08/2009: read the first line line = datasetFile.readline() diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 6bc0ef77..f74e655d 100755 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -43,7 +43,6 @@ from pprint import pformat as pf from htmlgen import HTMLgen2 as HT import reaper -from base import webqtlConfig from utility.THCell import THCell from utility.TDCell import TDCell from base.trait import GeneralTrait diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 40f518f0..61847bc3 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -26,8 +26,6 @@ import reaper from base.trait import GeneralTrait from base import data_set from base import species -from base import webqtlConfig -from utility import webqtlUtil # from wqflask.my_pylmm.pyLMM import lmm # from wqflask.my_pylmm.pyLMM import input from utility import helper_functions diff --git a/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py b/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py index ec9aa29c..f45ec0c4 100755 --- a/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py +++ b/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py @@ -45,40 +45,40 @@ class IntervalAnalystPage(templatePage): #A dictionary that lets us map the html form names "txStart_mm6" -> "Mb Start (mm8)" #the first item is the short name (column headers) and the second item is the long name (dropdown list) # [short name, long name, category] - columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'], + columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'], "GeneDescription" : ["Description", "Gene Description", 'species'], - 'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'], - 'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'], - 'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'], + 'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'], + 'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'], + 'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'], "ProteinID" : ["Prot ID", "Protein ID", 'protein'], - "Chromosome" : ["Chr", "Chromosome", 'species'], - "TxStart" : ["Start", "Mb Start", 'species'], - "TxEnd" : ["End", "Mb End", 'species'], - "GeneLength" : ["Length", "Kb Length", 'species'], - "cdsStart" : ["CDS Start", "Mb CDS Start", 'species'], + "Chromosome" : ["Chr", "Chromosome", 'species'], + "TxStart" : ["Start", "Mb Start", 'species'], + "TxEnd" : ["End", "Mb End", 'species'], + "GeneLength" : ["Length", "Kb Length", 'species'], + "cdsStart" : ["CDS Start", "Mb CDS Start", 'species'], "cdsEnd" : ["CDS End", "Mb CDS End", 'species'], - "exonCount" : ["Num Exons", "Exon Count", 'species'], - "exonStarts" : ["Exon Starts", "Exon Starts", 'species'], - "exonEnds" : ["Exon Ends", "Exon Ends", 'species'], - "Strand" : ["Strand", "Strand", 'species'], + "exonCount" : ["Num Exons", "Exon Count", 'species'], + "exonStarts" : ["Exon Starts", "Exon Starts", 'species'], + "exonEnds" : ["Exon Ends", "Exon Ends", 'species'], + "Strand" : ["Strand", "Strand", 'species'], "GeneID" : ["Gene ID", "Gene ID", 'species'], - "GenBankID" : ["GenBank", "GenBank ID", 'species'], + "GenBankID" : ["GenBank", "GenBank ID", 'species'], "UnigenID" : ["Unigen", "Unigen ID", 'species'], - "NM_ID" : ["NM ID", "NM ID", 'species'], + "NM_ID" : ["NM ID", "NM ID", 'species'], "kgID" : ["kg ID", "kg ID", 'species'], - "snpCount" : ["SNPs", "SNP Count", 'species'], - "snpDensity" : ["SNP Density", "SNP Density", 'species'], - "lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'], - "lod" : ["LOD", "Likelihood Odds Ratio", 'misc'], - "pearson" : ["Pearson", "Pearson Product Moment", 'misc'], - "literature" : ["Lit Corr", "Literature Correlation", 'misc'], + "snpCount" : ["SNPs", "SNP Count", 'species'], + "snpDensity" : ["SNP Density", "SNP Density", 'species'], + "lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'], + "lod" : ["LOD", "Likelihood Odds Ratio", 'misc'], + "pearson" : ["Pearson", "Pearson Product Moment", 'misc'], + "literature" : ["Lit Corr", "Literature Correlation", 'misc'], } ###Species Freeze speciesFreeze = {'mouse':'mm9', 'rat':'rn3', 'human':'hg19'} for key in speciesFreeze.keys(): speciesFreeze[speciesFreeze[key]] = key - + def __init__(self, fd): templatePage.__init__(self, fd) @@ -86,7 +86,7 @@ class IntervalAnalystPage(templatePage): fd.formdata['remote_ip'] = fd.remote_ip if not self.openMysql(): return - + self.species = fd.formdata.getvalue("species", "mouse") try: self.startMb = float(fd.formdata.getvalue("startMb")) @@ -96,7 +96,7 @@ class IntervalAnalystPage(templatePage): self.endMb = float(fd.formdata.getvalue("endMb")) except: self.endMb = self.startMb + 10 - + self.Chr = fd.formdata.getvalue("chromosome", "1") self.xls = fd.formdata.getvalue("xls", "1") try: @@ -107,38 +107,38 @@ class IntervalAnalystPage(templatePage): self.diffColDefault = self.diffCol = [] if self.species != 'mouse': self.diffColDefault = [2, 3]#default is B6 and D2 for other species - + controlFrm, dispFields = self.genControlForm(fd) geneTable, filename = self.genGeneTable(fd, dispFields) - + infoTD = HT.TD(width=400, valign= "top") - infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"), - HT.Strong("Species : "), self.species.title(), HT.BR(), - HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(), - HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(), + infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"), + HT.Strong("Species : "), self.species.title(), HT.BR(), + HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(), + HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(), ) if filename: infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize") , " output in MS excel format.") - + mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD(" ", width="")), cellpadding=10) mainTable.append(HT.TR(HT.TD(geneTable, colspan=3))) self.dict['body'] = HT.TD(mainTable) self.dict['title'] = "Interval Analyst" - + def genGeneTable(self, fd, dispFields): filename = "" if self.xls: #import pyXLWriter as xl filename = "IntAn_Chr%s_%2.6f-%2.6f" % (self.Chr, self.startMb, self.endMb) filename += ".xls" - + # Create a new Excel workbook workbook = xl.Writer(os.path.join(webqtlConfig.TMPDIR, filename)) worksheet = workbook.add_worksheet() titleStyle = workbook.add_format(align = 'left', bold = 0, size=18, border = 1, border_color="gray") headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, fg_color = 0x1E, color="white", border = 1, border_color="gray") - + ##Write title Info worksheet.write([0, 0], "GeneNetwork Interval Analyst Table", titleStyle) worksheet.write([1, 0], "%s%s" % (webqtlConfig.PORTADDR, os.path.join(webqtlConfig.CGIDIR, self._scriptfile))) @@ -148,12 +148,12 @@ class IntervalAnalystPage(templatePage): worksheet.write([4, 0], "Search by : %s" % fd.formdata['remote_ip']) worksheet.write([5, 0], "view region : Chr %s %2.6f - %2.6f Mb" % (self.Chr, self.startMb, self.endMb)) nTitleRow = 7 - + geneTable = HT.TableLite(Class="collap", cellpadding=5) headerRow = HT.TR(HT.TD(" ", Class="fs13 fwb ffl b1 cw cbrb", width="1")) if self.xls: worksheet.write([nTitleRow, 0], "Index", headingStyle) - + for ncol, column in enumerate(dispFields): if len(column) == 1: headerRow.append(HT.TD(self.columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) @@ -162,24 +162,24 @@ class IntervalAnalystPage(templatePage): worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) else: - headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), " (%s)" % self.speciesFreeze[column[1]], + headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), " (%s)" % self.speciesFreeze[column[1]], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center")) if self.xls: colTitle = self.columnNames[column[0]][0] + " (%s)" % self.speciesFreeze[column[1]] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) - #headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), - # "(%s %s)" % (column[1].title(), self.speciesFreeze[column[1]]), + #headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), + # "(%s %s)" % (column[1].title(), self.speciesFreeze[column[1]]), # Class="colorBlue", NOWRAP=1, align="Center")) geneTable.append(headerRow) - + geneCol = GeneUtil.loadGenes(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species) for gIndex, theGO in enumerate(geneCol): geneRow = HT.TR(HT.TD(gIndex+1, Class="fs12 fwn b1", align="right")) if self.xls: nTitleRow += 1 worksheet.write([nTitleRow, 0], gIndex + 1) - + for ncol, column in enumerate(dispFields): if len(column) == 1 or column[1]== self.species: keyValue = "" @@ -196,17 +196,17 @@ class IntervalAnalystPage(templatePage): curGO = theGO[subGO] if theGO[subGO].has_key(fieldName): keyValue = theGO[subGO][fieldName] - + if self.xls: worksheet.write([nTitleRow, ncol+1], keyValue) geneRow.append(self.formatTD(keyValue, fieldName, curSpecies, curGO)) - + geneTable.append(geneRow) - + if self.xls: workbook.close() return geneTable, filename - + def formatTD(self, keyValue, fieldName, Species, theGO): if keyValue is None: keyValue = "" @@ -219,7 +219,7 @@ class IntervalAnalystPage(templatePage): keyValue = "" return HT.TD(keyValue, Class="fs12 fwn b1", width=300) elif fieldName in ("GeneSymbol"): - webqtlLink = HT.Href("./%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.SCRIPTFILE, keyValue, Species), + webqtlLink = HT.Href("./%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.SCRIPTFILE, keyValue, Species), HT.Image("/images/webqtl_search.gif", border=0, valign="top"), target="_blank") if theGO['GeneID']: geneSymbolLink = HT.Href(webqtlConfig.NCBI_LOCUSID % theGO['GeneID'], keyValue, Class="normalsize", target="_blank") @@ -236,8 +236,8 @@ class IntervalAnalystPage(templatePage): return HT.TD(keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("snpCount"): if keyValue: - snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), - theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]), + snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), + theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]), text=theGO["snpCount"], target="_blank", Class="normalsize") else: snpString = keyValue @@ -252,13 +252,13 @@ class IntervalAnalystPage(templatePage): return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1) else: return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1,align="right") - + def genControlForm(self, fd): ##desc GeneList self.cursor.execute("Desc GeneList") GeneListFields = self.cursor.fetchall() GeneListFields = map(lambda X: X[0], GeneListFields) - + #group columns by category--used for creating the dropdown list of possible columns categories = {} for item in self.columnNames.keys(): @@ -267,7 +267,7 @@ class IntervalAnalystPage(templatePage): categories[category[-1]] = [item ] else: categories[category[-1]] = categories[category[-1]]+[item] - + ##List All Species in the Gene Table speciesDict = {} self.cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \ @@ -292,34 +292,34 @@ class IntervalAnalystPage(templatePage): pass AppliedField.append(item2) categories[specName] = AppliedField - + categoriesOrder += ['misc'] - + ############################################################ ## Create the list of possible columns for the dropdown list ############################################################ allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox") - + for category in categoriesOrder: allFields = categories[category] if allFields: geneOpt = HT.Optgroup(label=category.title()) for item in allFields: if category in self.speciesFreeze.keys(): - geneOpt.append(("%s (%s %s)" % (self.columnNames[item][1], category.title(), self.speciesFreeze[category]), + geneOpt.append(("%s (%s %s)" % (self.columnNames[item][1], category.title(), self.speciesFreeze[category]), "%s__%s" % (item, self.speciesFreeze[category]))) else: geneOpt.append((self.columnNames[item][1], item)) geneOpt.sort() allColumnsList.append(geneOpt) - + ###################################### ## Create the list of selected columns ###################################### - + #cols contains the value of all the selected columns submitCols = cols = fd.formdata.getvalue("columns", "default") - + if cols == "default": if self.species=="mouse": #these are the same columns that are shown on intervalPage.py cols = ['GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'Strand', 'GeneLength', 'GeneID', 'NM_ID', 'snpCount', 'snpDensity'] @@ -331,12 +331,12 @@ class IntervalAnalystPage(templatePage): else: if type(cols)==type(""): cols = [cols] - + colsLst = [] dispFields = [] for column in cols: if submitCols == "default" and column not in ('GeneSymbol') and (column in GeneListFields or column in speciesField): - colsLst.append(("%s (%s %s)" % (self.columnNames[column][1], self.species.title(), self.speciesFreeze[self.species]), + colsLst.append(("%s (%s %s)" % (self.columnNames[column][1], self.species.title(), self.speciesFreeze[self.species]), "%s__%s" % (column, self.speciesFreeze[self.species]))) dispFields.append([column, self.species]) else: @@ -346,17 +346,17 @@ class IntervalAnalystPage(templatePage): dispFields.append([column]) else: thisSpecies = self.speciesFreeze[column2[1]] - colsLst.append(("%s (%s %s)" % (self.columnNames[column2[0]][1], thisSpecies.title(), column2[1]), + colsLst.append(("%s (%s %s)" % (self.columnNames[column2[0]][1], thisSpecies.title(), column2[1]), column)) dispFields.append((column2[0], thisSpecies)) selectedColumnsList = HT.Select(name="columns", Class="snpBrowserSelectBox", multiple="true", data=colsLst, size=6) - + ########################## ## Create the columns form - ########################## + ########################## columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, self._scriptfile), enctype="multipart/form-data") columnsForm.append(HT.Input(type="hidden", name="fromdatabase", value= fd.formdata.getvalue("fromdatabase", "unknown"))) - columnsForm.append(HT.Input(type="hidden", name="species", value=self.species)) + columnsForm.append(HT.Input(type="hidden", name="species", value=self.species)) if self.diffCol: columnsForm.append(HT.Input(type="hidden", name="s1", value=self.diffCol[0])) columnsForm.append(HT.Input(type="hidden", name="s2", value=self.diffCol[1])) @@ -366,8 +366,8 @@ class IntervalAnalystPage(templatePage): removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)") upButton = HT.Input(type="button", name="up", value="Up", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex-1, this.form.columns)") downButton = HT.Input(type="button", name="down", value="Down", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex+1, this.form.columns)") - clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)") - submitButton = HT.Input(type="submit", value="Refresh", Class="button", onClick="selectAllElements(this.form.columns)") + clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)") + submitButton = HT.Input(type="submit", value="Refresh", Class="button", onClick="selectAllElements(this.form.columns)") selectChrBox = HT.Select(name="chromosome") self.cursor.execute(""" @@ -375,11 +375,11 @@ class IntervalAnalystPage(templatePage): Chr_Length.Name, Length from Chr_Length, Species where Chr_Length.SpeciesId = Species.Id AND - Species.Name = '%s' + Species.Name = '%s' Order by Chr_Length.OrderId """ % self.species) - + results = self.cursor.fetchall() for chrInfo in results: selectChrBox.append((chrInfo[0], chrInfo[0])) @@ -401,5 +401,5 @@ class IntervalAnalystPage(templatePage): #columnsForm.append(HT.Input(type="hidden", name="sort", value=diffCol), # HT.Input(type="hidden", name="identification", value=identification), # HT.Input(type="hidden", name="traitInfo", value=traitInfo)) - + return columnsForm, dispFields diff --git a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py index d02d80b3..455fcf95 100755 --- a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py +++ b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py @@ -140,7 +140,7 @@ class MarkerRegressionPage(templatePage): intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight)) gifmap = self.plotIntMappingForPLINK(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, plinkResultDict=plinkResultDict) - intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png') + intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png') intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap') TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200)) @@ -249,7 +249,7 @@ class MarkerRegressionPage(templatePage): intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight)) gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "") filename= webqtlUtil.genRandStr("Itvl_") - intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png') + intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png') intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap') ################################################################ @@ -458,7 +458,7 @@ class MarkerRegressionPage(templatePage): #plotBar(myCanvas,10,10,390,290,LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test',identification=fd.identification) Plot.plotBar(myCanvas, LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test') filename= webqtlUtil.genRandStr("Reg_") - myCanvas.save(webqtlConfig.IMGDIR+filename, format='gif') + myCanvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif') img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test') if fd.suggestive == None: diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 36334317..265f9473 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -30,7 +30,7 @@ from flask import Flask, g from base.trait import GeneralTrait from base import data_set from base import species -from base import webqtlConfig +# from base import webqtlConfig from utility import webqtlUtil from utility import helper_functions from utility import Plot, Bunch diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 01303b0f..decde579 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -178,8 +178,8 @@ class MarkerRegression(object): self.species = start_vars['species'] #Needing for form submission when doing single chr mapping or remapping after changing options - self.vals = start_vars['vals'] - self.mapping_method = start_vars['mapping_method'] + self.vals = start_vars['vals'] + self.mapping_method = start_vars['mapping_method'] if self.mapping_method == "rqtl_geno": self.mapmethod_rqtl_geno = start_vars['method'] self.mapmodel_rqtl_geno = start_vars['model'] @@ -232,7 +232,7 @@ class MarkerRegression(object): self.significant = start_vars['significant'] else: self.nperm = 0 - + if 'bootCheck' in start_vars.keys(): self.bootChecked = start_vars['bootCheck'] else: @@ -308,7 +308,7 @@ class MarkerRegression(object): if 'showSNP' in start_vars.keys(): self.SNPChecked = start_vars['showSNP'] else: - self.SNPChecked = False + self.SNPChecked = False if 'showGenes' in start_vars.keys(): self.geneChecked = start_vars['showGenes'] else: @@ -321,7 +321,7 @@ class MarkerRegression(object): self.endMb = float(start_vars['endMb']) except: self.endMb = -1 - try: + try: self.lrsMax = float(start_vars['lrsMax']) except: self.lrsMax = 0 @@ -363,7 +363,7 @@ class MarkerRegression(object): self.ChrList.append((indChr.name, i)) - + self.ChrLengthMbList = g.db.execute(""" Select Length from Chr_Length, InbredSet @@ -517,7 +517,7 @@ class MarkerRegression(object): chrName = self.selectedChr # Draw the genes for this chromosome / region of this chromosome webqtldatabase = self.dataset.name - + if self.dataset.group.species == "mouse": self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse") elif self.dataset.group.species == "rat": @@ -533,11 +533,11 @@ class MarkerRegression(object): # # #GENEID = fd.formdata.getvalue('GeneId') or None # GENEID = None - # + # # geneTableContainer = HT.Div(Id="sortable") #Div to hold table # geneTable = self.geneTable(self.geneCol,GENEID) # geneTableContainer.append(geneTable) - # + # # mainfmName = webqtlUtil.genRandStr("fm_") # tableForm = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden')) # tableForm.append(HT.Input(name='FormID', value='', type='hidden')) @@ -552,22 +552,22 @@ class MarkerRegression(object): #else: showLocusForm = "" intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight)) - gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm) + gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm) self.gifmap = gifmap.__str__() #print("GIFMAP:", gifmap.__str__()) self.filename= webqtlUtil.genRandStr("Itvl_") - intCanvas.save(os.path.join(webqtlConfig.IMGDIR, self.filename), format='jpeg') + intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg') intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap') #Scales plot differently for high resolution if self.draw2X: intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2)) gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2) - intCanvasX2.save(os.path.join(webqtlConfig.IMGDIR, self.filename+"X2"), format='png') + intCanvasX2.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename+"X2"), format='png') #DLintImgX2=HT.Href(text='Download',url = '/image/'+self.filename+'X2.png', Class='smallsize', target='_blank') - + #textUrl = self.writeQTL2Text(fd, self.filename) ################################################################ @@ -597,7 +597,7 @@ class MarkerRegression(object): showLocusForm.append(intImg) else: showLocusForm = intImg - + if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm: self.perm_filename = self.drawPermutationHistogram() #perm_text_file = self.permutationTextFile() @@ -667,7 +667,7 @@ class MarkerRegression(object): TD_LR.append(HT.Blockquote(tableForm)) self.body = TD_LR - + #self.dict['body'] = TD_LR #self.dict['title'] = "Mapping" @@ -858,7 +858,7 @@ class MarkerRegression(object): BootCoord = [] i = 0 startX = xLeftOffset - + if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes for j, _chr in enumerate(self.genotype): BootCoord.append( []) @@ -881,8 +881,8 @@ class MarkerRegression(object): else: Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale BootCoord[-1].append([Xc, self.bootResult[i]]) - i += 1 - + i += 1 + #reduce bootResult if self.selectedChr > -1: maxBootBar = 80.0 @@ -1411,7 +1411,7 @@ class MarkerRegression(object): if _strains[ii] in self.dataset.group.samplelist: temp = GeneralObject(name=_strains[ii], value=_val) smd.append(temp) - + smd.sort(lambda A, B: cmp(A.value, B.value)) smd.reverse() @@ -1566,14 +1566,14 @@ class MarkerRegression(object): firstGene = 0 else: lastGene = 0 - + for j, _geno in enumerate (self.genotype[0][1].genotype): plotbxd=0 for item in smd: if item.name == samplelist[j]: - plotbxd=1 - + plotbxd=1 + if (plotbxd == 1): ind = 0 @@ -1620,28 +1620,28 @@ class MarkerRegression(object): currentChromosome = self.genotype[0].name i = 0 - + paddingTop = yTopOffset ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING - + if zoom == 1: for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep): - + calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth) - + xBrowse1 = pixel xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1)) - + WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT)) bandWidth = xBrowse2 - xBrowse1 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) - + WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE)) canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR) canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) - + UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT)) if self.species == "mouse": UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) @@ -1651,7 +1651,7 @@ class MarkerRegression(object): gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE)) canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR) canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR) - + ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT)) if self.species == "mouse": ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) @@ -1766,7 +1766,7 @@ class MarkerRegression(object): ChrAInfo = [] preLpos = -1 distinctCount = 0.0 - + #if len(self.genotype) > 1: if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes for i, _chr in enumerate(self.genotype): @@ -1809,7 +1809,7 @@ class MarkerRegression(object): offsetA = -stepA lineColor = pid.lightblue startPosX = xLeftOffset - + for j, ChrInfo in enumerate(ChrAInfo): preLpos = -1 for i, item in enumerate(ChrInfo): @@ -1877,7 +1877,7 @@ class MarkerRegression(object): # lodm = self.LODFACTOR # else: # lodm = 1.0 - + #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD if self.lrsMax <= 0: #sliding scale if "lrs_value" in self.qtlresults[0]: @@ -1890,7 +1890,7 @@ class MarkerRegression(object): else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: self.significant = min(self.significant, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) else: pass else: @@ -1903,10 +1903,10 @@ class MarkerRegression(object): else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: self.significant = min(self.significant, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) else: pass - + if self.permChecked and self.nperm > 0 and not self.multipleInterval: LRS_LOD_Max = max(self.significant, LRS_LOD_Max) @@ -1923,7 +1923,7 @@ class MarkerRegression(object): LRSScale = 2.5 else: LRSScale = 1.0 - + LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) #make sure the user's value appears on the y-axis #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460 @@ -1953,7 +1953,7 @@ class MarkerRegression(object): #"Significant" and "Suggestive" Drawing Routine # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...) - + #ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist): rightEdge = int(start_pos_x + chr_length_dist*plotXScale - self.SUGGESTIVE_WIDTH/1.5) @@ -1976,13 +1976,13 @@ class MarkerRegression(object): start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale return start_pos_x - + for i, _chr in enumerate(self.genotype): if self.selectedChr != -1: if _chr.name == self.ChrList[self.selectedChr][0]: startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[0]) break - else: + else: continue else: startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[i]) @@ -1997,7 +1997,7 @@ class MarkerRegression(object): #else: # dominanceMax = -1 lrsEdgeWidth = 2 - + if zoom == 2: lrsEdgeWidth = 2 * lrsEdgeWidth @@ -2018,7 +2018,7 @@ class MarkerRegression(object): if qtlresult['chr'] != previous_chr and self.selectedChr == -1: if self.manhattan_plot != True: canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - + if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE @@ -2048,7 +2048,7 @@ class MarkerRegression(object): canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) else: canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - + LRSCoordXY = [] AdditiveCoordXY = [] previous_chr = qtlresult['chr'] @@ -2061,7 +2061,7 @@ class MarkerRegression(object): #startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale - #for j, _chr in enumerate(self.genotype): + #for j, _chr in enumerate(self.genotype): #ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used if self.plotScale == "physic": this_chr = str(self.ChrList[self.selectedChr][0]) @@ -2126,7 +2126,7 @@ class MarkerRegression(object): if self.manhattan_plot != True: canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - + if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE @@ -2156,7 +2156,7 @@ class MarkerRegression(object): canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) else: canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - + if not self.multipleInterval and INTERCROSS and self.dominanceChecked: plusColor = self.DOMINANCE_COLOR_POSITIVE minusColor = self.DOMINANCE_COLOR_NEGATIVE @@ -2186,7 +2186,7 @@ class MarkerRegression(object): canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) else: canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - + ###draw additive scale if not self.multipleInterval and self.additiveChecked: @@ -2222,7 +2222,7 @@ class MarkerRegression(object): if zoom == 2: fontZoom = 1.5 yTopOffset += 30 - + #calculate plot scale if self.plotScale != 'physic': self.ChrLengthDistList = self.ChrLengthCMList @@ -2589,13 +2589,13 @@ class MarkerRegression(object): perm_output = [value/4.16 for value in self.perm_output] else: perm_output = self.perm_output - + Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test') filename= webqtlUtil.genRandStr("Reg_") myCanvas.save(webqtlConfig.IMGDIR+filename, format='gif') - + return filename - + # img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test') # self.suggestive = self.perm_output[int(self.nperm*0.37-1)] @@ -2609,9 +2609,9 @@ class MarkerRegression(object): # permutation.append(HT.TR(HT.TD(img)), # HT.TR(HT.TD('')), # HT.TR(HT.TD('Total of %d permutations'%self.nperm))) - + # return permutation - + def permutationTextFile(self): filename= webqtlUtil.genRandStr("Reg_") fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb') @@ -2624,12 +2624,12 @@ class MarkerRegression(object): '    Significant LRS =%3.2f\n'%self.significant, HT.BR(), '    Highly Significant LRS =%3.2f\n' % self.highlysignificant) - + for lrs_value in self.perm_output: fpText.write(str(lrs_value) + "\n") - + textUrl = HT.Href(text = 'Download Permutation Results', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn') - + return textUrl def geneTable(self, geneCol, refGene=None): @@ -2654,7 +2654,7 @@ class MarkerRegression(object): else: gene_table = "" - return gene_table + return gene_table def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None): if not geneId1 or not geneId2: @@ -2954,4 +2954,4 @@ And by voluntary, according to HFG when I talked to him, they have a choice betw sortby = ("", "") - return sortby \ No newline at end of file + return sortby diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 52fe2e34..9941a4d3 100755 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -26,7 +26,6 @@ from MySQLdb import escape_string as escape # Instead of importing HT we're going to build a class below until we can eliminate it # from htmlgen import HTMLgen2 as HT -from base import webqtlConfig from utility.benchmark import Bench from base.data_set import create_dataset from base.trait import GeneralTrait diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 35f7fe5f..e80cf191 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -166,7 +166,7 @@ class ShowTrait(object): return False def check_pylmm_rqtl(): - if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.NEWGENODIR+self.dataset.group.name+".json") > 0): + if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.JSON_GENODIR+self.dataset.group.name+".json") > 0): return True else: return False -- cgit v1.2.3 From 31a1c126185adb747028d035717ad72728a52b0e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 24 Feb 2016 11:25:10 +0000 Subject: -a [PATCH 038/100] Fix compile errors --- wqflask/base/data_set.py | 6 +++--- wqflask/utility/tools.py | 6 ++++-- 2 files changed, 7 insertions(+), 5 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 6527657a..8b2a9f01 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import locate, locate_without_error +from utility.tools import locate, locate_ignore_error from maintenance import get_group_samplelists @@ -405,8 +405,8 @@ class DatasetGroup(object): else: print("Cache not hit") - genotype_fn = locate_without_error(self.name+".geno",'genotype') - mapping_fn = locate_without_error(self.name+".fam",'mapping') + genotype_fn = locate_ignore_error(self.name+".geno",'genotype') + mapping_fn = locate_ignore_error(self.name+".fam",'mapping') if mapping_fn: self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn) elif genotype_fn: diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index c0f6a49a..67c5128a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -1,3 +1,4 @@ + # Tools/paths finder resolves external paths from settings and/or environment # variables @@ -83,9 +84,10 @@ def assert_dir(dir): if not valid_path(dir): raise Exception("ERROR: can not find directory "+dir) return dir - + def mk_dir(dir): - os.makedirs(dir) + if not valid_path(dir): + os.makedirs(dir) return assert_dir(dir) def locate(name, subdir=None): -- cgit v1.2.3 From 575e00b1061c58952cba38af5ab078ca0081b4d7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 24 Feb 2016 16:34:52 +0000 Subject: [PATCH 041/100] Fixes for running tools --- etc/default_settings.py | 6 +++--- wqflask/utility/tools.py | 4 ++-- wqflask/wqflask/marker_regression/marker_regression.py | 3 +-- wqflask/wqflask/marker_regression/marker_regression_gn1.py | 7 ++++--- 4 files changed, 10 insertions(+), 10 deletions(-) (limited to 'wqflask/utility') diff --git a/etc/default_settings.py b/etc/default_settings.py index 6a218f26..60a3a7b4 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -24,6 +24,6 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a # Path overrides for Genenetwork GENENETWORK_FILES = "../../gn2_data" -PYLMM_COMMAND = os.popen("which pylmm_redis").read() -PLINK_COMMAND = os.popen("which plink2").read() -GEMMA_COMMAND = os.popen("which gemma").read() +PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) +PLINK_COMMAND = str.strip(os.popen("which plink2").read()) +GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 67c5128a..51189fa3 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -133,7 +133,7 @@ def tempdir(): # Cached values PYLMM_COMMAND = pylmm_command() -GEMMA_COMMAND = pylmm_command() -PLINK_COMMAND = pylmm_command() +GEMMA_COMMAND = gemma_command() +PLINK_COMMAND = plink_command() FLAT_FILES = flat_files() TEMPDIR = tempdir() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 265f9473..910d0c3c 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -937,8 +937,7 @@ class MarkerRegression(object): Redis.expire(key, 60*60) print("before printing command") - command = PYLMM_COMMAND + ' --key {} --species {}'.format(key, - "other") + command = PYLMM_COMMAND + ' --key {} --species {}'.format(key, "other") print("command is:", command) print("after printing command") diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index decde579..4edc1891 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -28,6 +28,7 @@ import time import string from math import * import piddle as pid +import piddlePIL as pil import sys,os import cPickle import httplib, urllib @@ -551,7 +552,7 @@ class MarkerRegression(object): # showLocusForm = webqtlUtil.genRandStr("fm_") #else: showLocusForm = "" - intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight)) + intCanvas = pil.PILCanvas(size=(self.graphWidth, self.graphHeight)) gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm) self.gifmap = gifmap.__str__() @@ -563,7 +564,7 @@ class MarkerRegression(object): #Scales plot differently for high resolution if self.draw2X: - intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2)) + intCanvasX2 = pil.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2)) gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename+"X2"), format='png') #DLintImgX2=HT.Href(text='Download',url = '/image/'+self.filename+'X2.png', Class='smallsize', target='_blank') @@ -2582,7 +2583,7 @@ class MarkerRegression(object): ######################################### # Permutation Graph ######################################### - myCanvas = pid.PILCanvas(size=(400,300)) + myCanvas = pil.PILCanvas(size=(400,300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": perm_output = [value*4.16 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": -- cgit v1.2.3 From 9395e9f3cc2d06e069c5de797b2d6e8e59cfba7c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 24 Feb 2016 17:00:04 +0000 Subject: [PATCH 042/100] Sanitizing locations --- wqflask/utility/tools.py | 5 ++--- wqflask/wqflask/marker_regression/marker_regression.py | 13 ++++++------- 2 files changed, 8 insertions(+), 10 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 51189fa3..b8eff12a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -1,4 +1,3 @@ - # Tools/paths finder resolves external paths from settings and/or environment # variables @@ -105,9 +104,9 @@ def locate(name, subdir=None): print("Found: file "+lookfor+"\n") return lookfor else: - raise IOError("Can not locate "+lookfor) + raise Exception("Can not locate "+lookfor) if subdir: sys.stderr.write(subdir) - raise IOError("Can not locate "+name+" in "+base) + raise Exception("Can not locate "+name+" in "+base) def locate_ignore_error(name, subdir=None): """ diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 910d0c3c..e9cfb06d 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -41,7 +41,8 @@ from wqflask.marker_regression import gemma_mapping #from wqflask.marker_regression import plink_mapping #from wqflask.marker_regression import rqtl_mapping -from utility.tools import locate, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND +from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND +from utility.external import shell class MarkerRegression(object): @@ -413,8 +414,8 @@ class MarkerRegression(object): write_cross = ro.r["write.cross"] # Map the write.cross function GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the GENOtoCSVR function - genofilelocation = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".geno" - crossfilelocation = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".cross" + genofilelocation = locate(self.dataset.group.name + ".geno", "genotype") + crossfilelocation = locate(self.dataset.group.name + ".cross", "genotype") #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation) @@ -860,9 +861,7 @@ class MarkerRegression(object): Redis.expire(key, 60*60) command = PYLMM_COMMAND+' --key {} --species {}'.format(key,"other") - - os.system(command) - + shell(command) json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60) results = json.loads(json_results[1]) @@ -941,7 +940,7 @@ class MarkerRegression(object): print("command is:", command) print("after printing command") - os.system(command) + shell(command) #t_stats, p_values = lmm.run(key) #lmm.run(key) -- cgit v1.2.3 From e42b21c66b09128ac6a9c18ca018287516d8c309 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Wed, 24 Feb 2016 17:41:55 +0000 Subject: Minor fixes --- wqflask/utility/external.py | 9 +++++++++ wqflask/wqflask/marker_regression/marker_regression_gn1.py | 5 +++-- 2 files changed, 12 insertions(+), 2 deletions(-) create mode 100644 wqflask/utility/external.py (limited to 'wqflask/utility') diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py new file mode 100644 index 00000000..bd8cf584 --- /dev/null +++ b/wqflask/utility/external.py @@ -0,0 +1,9 @@ +# Call external program + +import os +import sys +import subprocess + +def shell(command): + if not subprocess.call(command, shell=True): + raise Exception("ERROR: failed on "+command) diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 4edc1891..a68c9586 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -29,6 +29,7 @@ import string from math import * import piddle as pid import piddlePIL as pil +from piddle import Font import sys,os import cPickle import httplib, urllib @@ -941,7 +942,7 @@ class MarkerRegression(object): bootScale = bootScale[:-1] + [highestPercent] bootOffset = 50*fontZoom - bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0) + bootScaleFont=Font(ttf="verdana",size=13*fontZoom,bold=0) canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow) canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black) canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black) @@ -2259,7 +2260,7 @@ class MarkerRegression(object): chrFontZoom = 2 else: chrFontZoom = 1 - chrLabelFont=pid.Font(ttf="verdana",size=24*chrFontZoom,bold=0) + chrLabelFont=Font(ttf="verdana",size=24*chrFontZoom,bold=0) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): -- cgit v1.2.3 From 2e039da988b585fde5a09e94d7fd7b56262752f2 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 25 Feb 2016 11:22:02 +0000 Subject: external program should fail on return value not zero --- wqflask/utility/external.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py index bd8cf584..50afea08 100644 --- a/wqflask/utility/external.py +++ b/wqflask/utility/external.py @@ -5,5 +5,5 @@ import sys import subprocess def shell(command): - if not subprocess.call(command, shell=True): + if subprocess.call(command, shell=True) != 0: raise Exception("ERROR: failed on "+command) -- cgit v1.2.3 From a66858e99c2195d90a187899db6f4dd8966a0a2c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 3 Mar 2016 11:21:01 +0000 Subject: Show error when GENODIR is missing --- bin/genenetwork2 | 13 +++++++------ etc/default_settings.py | 2 +- wqflask/utility/tools.py | 4 ++-- 3 files changed, 10 insertions(+), 9 deletions(-) (limited to 'wqflask/utility') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index a0a013fc..bbb2a19f 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -9,18 +9,19 @@ SCRIPT=$(readlink -f "$0") # Absolute path this script is in, thus /home/user/bin GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT")) + +GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg +if [ -d $GN2_GUIX_PATH ]; then + GN2_BASE_PATH=$GN2_GUIX_PATH +fi echo $GN2_BASE_PATH # Handle settings parameter settings=$1 if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi if [ ! -e $settings ]; then - GN2_BASE_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg - settings=$GN2_BASE_PATH/etc/default_settings.py - if [ ! -e $settings ]; then - echo "ERROR: can not locate settings file - pass it in the command line" - exit 1 - fi + echo "ERROR: can not locate settings file - pass it in the command line" + exit 1 fi export WQFLASK_SETTINGS=$settings diff --git a/etc/default_settings.py b/etc/default_settings.py index 60a3a7b4..0cf40265 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -23,7 +23,7 @@ SERVER_PORT = 5003 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' # Path overrides for Genenetwork -GENENETWORK_FILES = "../../gn2_data" +GENENETWORK_FILES = os.environ['HOME']+"/gn2_data" PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) PLINK_COMMAND = str.strip(os.popen("which plink2").read()) GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index b8eff12a..9405a9c6 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -76,8 +76,8 @@ def plink_command(guess=None): def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: - return valid_path(base+"/"+subdir) - return valid_path(base) + return assert_dir(base+"/"+subdir) + return assert_dir(base) def assert_dir(dir): if not valid_path(dir): -- cgit v1.2.3 From a13baa5fb98d8167e70df7008d0d07b40a05a6b9 Mon Sep 17 00:00:00 2001 From: DannyArends Date: Tue, 22 Mar 2016 23:37:13 +0100 Subject: Adding the geno file parser from Zach --- wqflask/utility/genofile_parser.py | 96 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 wqflask/utility/genofile_parser.py (limited to 'wqflask/utility') diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py new file mode 100644 index 00000000..9dd7b08b --- /dev/null +++ b/wqflask/utility/genofile_parser.py @@ -0,0 +1,96 @@ +# CTL analysis for GN2 +# Author / Maintainer: Danny Arends + +from __future__ import print_function, division, absolute_import +import sys +import os +import glob +import traceback +import gzip + +import simplejson as json + +from pprint import pformat as pf + +class Marker(object): + def __init__(self): + self.name = None + self.chr = None + self.cM = None + self.Mb = None + self.genotypes = [] + + +class ConvertGenoFile(object): + + def __init__(self, input_file): + self.mb_exists = False + self.cm_exists = False + self.markers = [] + + self.latest_row_pos = None + self.latest_col_pos = None + + self.latest_row_value = None + self.latest_col_value = None + self.input_fh = open(input_file) + print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!") + self.haplotype_notation = { + '@mat': "3", + '@pat': "1", + '@het': "2", + '@unk': "NA" + } + self.configurations = {} + + def process_rows(self): + for self.latest_row_pos, row in enumerate(self.input_fh): + self.latest_row_value = row + # Take care of headers + if not row.strip(): + continue + if row.startswith('#'): + continue + if row.startswith('Chr'): + if 'Mb' in row.split(): + self.mb_exists = True + if 'cM' in row.split(): + self.cm_exists = True + continue + if row.startswith('@'): + key, _separater, value = row.partition(':') + key = key.strip() + value = value.strip() + if key in self.haplotype_notation: + self.configurations[value] = self.haplotype_notation[key] + continue + if not len(self.configurations): + raise EmptyConfigurations + yield row + + def process_csv(self): + for row_count, row in enumerate(self.process_rows()): + row_items = row.split("\t") + + this_marker = Marker() + this_marker.name = row_items[1] + this_marker.chr = row_items[0] + if self.cm_exists and self.mb_exists: + this_marker.cM = row_items[2] + this_marker.Mb = row_items[3] + genotypes = row_items[4:] + elif self.cm_exists: + this_marker.cM = row_items[2] + genotypes = row_items[3:] + elif self.mb_exists: + this_marker.Mb = row_items[2] + genotypes = row_items[3:] + else: + genotypes = row_items[2:] + for item_count, genotype in enumerate(genotypes): + if genotype.upper() in self.configurations: + this_marker.genotypes.append(self.configurations[genotype.upper()]) + else: + this_marker.genotypes.append("NA") + self.markers.append(this_marker.__dict__) + -- cgit v1.2.3 From 3d505d997511cd8f7b9f14510059cb2983edc6d4 Mon Sep 17 00:00:00 2001 From: DannyArends Date: Wed, 23 Mar 2016 23:07:16 +0100 Subject: Parsing the names of the individuals, and coding H as -999 --- wqflask/utility/genofile_parser.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index 9dd7b08b..67b84dc9 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -8,6 +8,7 @@ import glob import traceback import gzip + import simplejson as json from pprint import pformat as pf @@ -34,12 +35,12 @@ class ConvertGenoFile(object): self.latest_row_value = None self.latest_col_value = None self.input_fh = open(input_file) - print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!") + print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") self.haplotype_notation = { - '@mat': "3", - '@pat': "1", - '@het': "2", - '@unk': "NA" + '@mat': "1", + '@pat': "2", + '@het': "-999", + '@unk': "-999" } self.configurations = {} @@ -56,6 +57,8 @@ class ConvertGenoFile(object): self.mb_exists = True if 'cM' in row.split(): self.cm_exists = True + skip = 2 + self.cm_exists + self.mb_exists + self.individuals = row.split()[skip:] continue if row.startswith('@'): key, _separater, value = row.partition(':') @@ -88,9 +91,10 @@ class ConvertGenoFile(object): else: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): - if genotype.upper() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper()]) + if genotype.upper().strip() in self.configurations: + this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) else: + print("WARNING:", genotype.upper()) this_marker.genotypes.append("NA") self.markers.append(this_marker.__dict__) -- cgit v1.2.3 From 28ccde8e417b965710bbeef48d468a6b717c10a4 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 10:44:10 +0000 Subject: A few fixes to get the webserver running again --- doc/README.org | 11 ++++++++--- wqflask/utility/tools.py | 1 - wqflask/wqflask/marker_regression/gemma_mapping.py | 4 +--- wqflask/wqflask/marker_regression/marker_regression.py | 4 ++-- 4 files changed, 11 insertions(+), 9 deletions(-) (limited to 'wqflask/utility') diff --git a/doc/README.org b/doc/README.org index ee54f781..3b96717f 100644 --- a/doc/README.org +++ b/doc/README.org @@ -134,12 +134,17 @@ configuration. ** Run your own copy of GN2 -At some point you may want to fix the source code. Clone the GN2 -repository from https://github.com/genenetwork/genenetwork2_diet +At some point you may want to fix the source code. Assuming you have +Guix and Genenetwork2 installed (as described above) clone the GN2 +repository from https://github.com/genenetwork/genenetwork2_diet + +Copy the paths into your terminal from (mainly so PYTHON_PATH and +R_LIBS_SITE are set) + +: guix package --search-paths Inside the repository: -: git clone : cd genenetwork2_diet : ./bin/genenetwork2 diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 9405a9c6..dd8c4a1e 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -5,7 +5,6 @@ import os import sys from wqflask import app - def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with get_valid_path is a function checking whether the diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index ae426621..8fb086c1 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -1,9 +1,7 @@ import os from base import webqtlConfig -from utility.tools import gemma_command - -GEMMA_PATH,GEMMA_COMMAND = gemma_command() +from utility.tools import GEMMA_COMMAND def run_gemma(this_dataset, samples, vals): """Generates p-values for each marker using GEMMA""" diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 39d7c78a..97949f93 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -1103,5 +1103,5 @@ def get_markers_from_csv(included_markers, p_values, group_name): return markers - if __name__ == '__main__': - import cPickle as pickle +if __name__ == '__main__': + import cPickle as pickle -- cgit v1.2.3