diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 12 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_probesetfreeze_file.py | 2 | ||||
| -rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 12 | ||||
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 6 |
4 files changed, 16 insertions, 16 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..fd65a52a 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -41,7 +41,7 @@ from __future__ import print_function, division import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -50,7 +50,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI import MySQLdb import simplejson as json -import urlparse +import urllib.parse #import sqlalchemy as sa @@ -66,7 +66,7 @@ from pprint import pformat as pf def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -108,7 +108,7 @@ def get_types(groups): """Build types list""" types = {} #print("Groups: ", pf(groups)) - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code @@ -195,9 +195,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b7b2dc8e..4231cc7c 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -82,7 +82,7 @@ def get_probeset_vals(cursor, dataset_name): def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) - first_probeset = list(probeset_vals.itervalues())[0] + first_probeset = list(probeset_vals.values())[0] print("\n**** first_probeset is:", pf(first_probeset)) for strain in strains: print("\n**** strain is:", pf(strain)) diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 41a3aad8..4d6e03bf 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,12 +1,12 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.insert(0,'./') +sys.path.insert(0, './') + -from itertools import izip import MySQLdb -import urlparse +import urllib.parse import numpy as np import pandas as pd @@ -22,7 +22,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -37,7 +37,7 @@ def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) - input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=range(1, ncols)) + input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) #This function taken from https://github.com/ShawnLYU/Quantile_Normalize @@ -60,7 +60,7 @@ def set_data(dataset_name): sample_list = [] with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh: - for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)): + for i, (line1, line2) in enumerate(zip(orig_fh, quant_fh)): trait_dict = {} sample_list = [] if i == 0: diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 54fd8e7e..abd5416c 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -22,7 +22,7 @@ import sys import json # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -34,7 +34,7 @@ Redis = get_redis_conn() import MySQLdb -import urlparse +import urllib.parse from utility.logger import getLogger logger = getLogger(__name__) @@ -42,7 +42,7 @@ logger = getLogger(__name__) def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], |