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
48
49
50
51
52
53
54
55
56
57
58
59
60
|
#!/usr/bin/python
"""
Generate relatedness matrix files for GEMMA from BIMBAM genotype/phenotype files
This file goes through all of the BIMBAM files in the bimbam diretory
and uses GEMMA to generate their corresponding kinship/relatedness matrix file
"""
import sys
sys.path.append("..")
import os
import glob
class GenerateKinshipMatrices(object):
def __init__(self, group_name, geno_file, pheno_file):
self.group_name = group_name
self.geno_file = geno_file
self.pheno_file = pheno_file
def generate_kinship(self):
gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + " -p " + self.pheno_file + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
print("command:", gemma_command)
os.system(gemma_command)
@classmethod
def process_all(self, geno_dir, bimbam_dir):
os.chdir(geno_dir)
for input_file in glob.glob("*"):
if not input_file.endswith(('geno', '.geno.gz')):
continue
group_name = ".".join(input_file.split('.')[:-1])
if group_name == "HSNIH-Palmer":
continue
geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt")
pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt")
convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file)
try:
convertob.generate_kinship()
except EmptyConfigurations as why:
print(" No config info? Continuing...")
continue
except Exception as why:
print(" Exception:", why)
print(traceback.print_exc())
print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
convertob.latest_col_pos))
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
if __name__=="__main__":
Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
#./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
|
