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from __future__ import absolute_import, print_function, division
import os
import glob
import gzip
from base import webqtlConfig
def get_sample_list_dir(geno_dir="/home/zas1024/gene/web/genotypes/"):
os.chdir(geno_dir)
for group_file in glob.glob("*"):
if group_file.lower().endswith(('.geno', '.geno.gz')):
#group_name = genofilename.split('.')[0]
sample_list = get_sample_list(group_file)
print("\n\n{}\n\n".format(sample_list))
def get_sample_list(group_file):
print(group_file)
genofilename = str(os.path.join(webqtlConfig.GENODIR, group_file))
if genofilename.lower().endswith('.geno.gz'):
genofile = gzip.open(genofilename)
else:
genofile = open(genofilename)
for line in genofile:
line = line.strip()
if not line:
continue
if line.startswith(("#", "@")):
continue
headline = line
break
headers = headline.split("\t")
if headers[3] == "Mb":
samplelist = headers[4:]
else:
samplelist = headers[3:]
return samplelist
if __name__ == '__main__':
get_sample_list_dir()
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