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authorBonfaceKilz2020-10-27 01:18:38 +0300
committerGitHub2020-10-27 01:18:38 +0300
commit37c391bc62e9080effcf83c6ff0056ab8841b7fb (patch)
tree1e794c5616c25e82869314a2f4e91f64c4d40ea9 /wqflask/maintenance/quantile_normalize.py
parent85896707ef1f9e214b45298f6b5b1a9dc37bc839 (diff)
parentb369489e6c075eee3f58bb33e493c901b052b0a1 (diff)
downloadgenenetwork2-37c391bc62e9080effcf83c6ff0056ab8841b7fb.tar.gz
Merge pull request #422 from BonfaceKilz/build/python3-migration
Build/python3 migration
Diffstat (limited to 'wqflask/maintenance/quantile_normalize.py')
-rw-r--r--wqflask/maintenance/quantile_normalize.py17
1 files changed, 6 insertions, 11 deletions
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)