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from __future__ import absolute_import, print_function, division
import os
import glob
import gzip
from base import webqtlConfig
def process_genofiles(geno_dir=webqtlConfig.GENODIR):
print("Yabba")
#sys.exit("Dabba")
os.chdir(geno_dir)
for geno_file in glob.glob("*"):
if geno_file.lower().endswith(('.geno', '.geno.gz')):
#group_name = genofilename.split('.')[0]
sample_list = get_samplelist(geno_file)
def get_samplelist(file_type, geno_file):
if file_type == "geno":
return get_samplelist_from_geno(geno_file)
elif file_type == "plink":
return get_samplelist_from_plink(geno_file)
def get_samplelist_from_geno(genofilename):
if os.path.isfile(genofilename + '.gz'):
genofilename += '.gz'
genofile = gzip.open(genofilename)
else:
genofile = open(genofilename)
for line in genofile:
line = line.strip()
if not line:
continue
if line.startswith(("#", "@")):
continue
break
headers = line.split()
if headers[3] == "Mb":
samplelist = headers[4:]
else:
samplelist = headers[3:]
return samplelist
def get_samplelist_from_plink(genofilename):
genofile = open(genofilename)
samplelist = []
for line in genofile:
line = line.split(" ")
samplelist.append(line[1])
return samplelist
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