diff options
Diffstat (limited to 'wqflask/maintenance/quantile_normalize.py')
| -rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 17 |
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) |