diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/convert_dryad_to_bimbam.py | 3 | ||||
| -rw-r--r-- | wqflask/maintenance/convert_geno_to_bimbam.py | 3 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 22 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_kinship_from_bimbam.py | 3 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_probesetfreeze_file.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/geno_to_json.py | 3 | ||||
| -rw-r--r-- | wqflask/maintenance/get_group_samplelists.py | 2 | ||||
| -rw-r--r-- | wqflask/maintenance/print_benchmark.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 17 | ||||
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 10 |
10 files changed, 23 insertions, 48 deletions
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py index e833b395..12ce35e9 100644 --- a/wqflask/maintenance/convert_dryad_to_bimbam.py +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") @@ -67,4 +66,4 @@ def convert_dryad_to_bimbam(filename): if __name__=="__main__": input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" - convert_dryad_to_bimbam(input_filename)
\ No newline at end of file + convert_dryad_to_bimbam(input_filename) diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 528b98cf..d49742f2 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -9,7 +9,6 @@ code """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -187,4 +186,4 @@ if __name__=="__main__": #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") #convertob.convert() ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) - #ConvertGenoFiles(Geno_Directory)
\ No newline at end of file + #ConvertGenoFiles(Geno_Directory) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..544e2fd1 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -30,18 +30,10 @@ It needs to be run manually when database has been changed. Run it as # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import print_function, division - -#from flask import config -# -#cdict = {} -#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') -#print("cdict is:", cdict) - import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -50,7 +42,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI import MySQLdb import simplejson as json -import urlparse +import urllib.parse #import sqlalchemy as sa @@ -66,7 +58,7 @@ from pprint import pformat as pf def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -108,7 +100,7 @@ def get_types(groups): """Build types list""" types = {} #print("Groups: ", pf(groups)) - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code @@ -195,9 +187,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) @@ -319,4 +311,4 @@ def _test_it(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main()
\ No newline at end of file + main() diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index b53f5dda..60257b28 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -8,7 +8,6 @@ and uses GEMMA to generate their corresponding kinship/relatedness matrix file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -58,4 +57,4 @@ if __name__=="__main__": Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/""" GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory) - #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
\ No newline at end of file + #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b7b2dc8e..b1e41e9a 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -1,7 +1,5 @@ #!/usr/bin/python -from __future__ import absolute_import, print_function, division - import sys # sys.path.insert(0, "..") - why? @@ -82,7 +80,7 @@ def get_probeset_vals(cursor, dataset_name): def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) - first_probeset = list(probeset_vals.itervalues())[0] + first_probeset = list(probeset_vals.values())[0] print("\n**** first_probeset is:", pf(first_probeset)) for strain in strains: print("\n**** strain is:", pf(strain)) diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 9579812a..7e7fd241 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -9,7 +9,6 @@ code """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -194,4 +193,4 @@ if __name__=="__main__": ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) #ConvertGenoFiles(Geno_Directory) - #process_csv(Input_File, Output_File)
\ No newline at end of file + #process_csv(Input_File, Output_File) diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index fb22898a..3f9d0278 100644 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import os import glob import gzip diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py index ae327cf3..b24ce4f1 100644 --- a/wqflask/maintenance/print_benchmark.py +++ b/wqflask/maintenance/print_benchmark.py @@ -1,7 +1,5 @@ #!/usr/bin/python -from __future__ import absolute_import, print_function, division - import time from pprint import pformat as pf @@ -40,4 +38,4 @@ def new_main(): print(pf(TheCounter.Counters)) if __name__ == '__main__': - new_main()
\ No newline at end of file + new_main() diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 41a3aad8..701b2b50 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,12 +1,7 @@ -from __future__ import absolute_import, print_function, division - import sys -sys.path.insert(0,'./') - -from itertools import izip - +sys.path.insert(0, './') import MySQLdb -import urlparse +import urllib.parse import numpy as np import pandas as pd @@ -22,7 +17,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -37,7 +32,7 @@ def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) - input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=range(1, ncols)) + input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) #This function taken from https://github.com/ShawnLYU/Quantile_Normalize @@ -60,7 +55,7 @@ def set_data(dataset_name): sample_list = [] with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh: - for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)): + for i, (line1, line2) in enumerate(zip(orig_fh, quant_fh)): trait_dict = {} sample_list = [] if i == 0: @@ -126,4 +121,4 @@ if __name__ == '__main__': } ) - print(response)
\ No newline at end of file + print(response) diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 54fd8e7e..4177c124 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -16,13 +16,11 @@ To run: """ -from __future__ import print_function, division - import sys import json # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -34,7 +32,7 @@ Redis = get_redis_conn() import MySQLdb -import urlparse +import urllib.parse from utility.logger import getLogger logger = getLogger(__name__) @@ -42,7 +40,7 @@ logger = getLogger(__name__) def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -163,4 +161,4 @@ def main(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main()
\ No newline at end of file + main() |