blob: 0a450d3fe2e5752573d566692078ead71138df6f (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
import os
import glob
import gzip
from base import webqtlConfig
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("\t")
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
|
