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authorArthur Centeno2021-06-15 15:33:59 +0000
committerArthur Centeno2021-06-15 15:33:59 +0000
commitc1a6ca69f7c48d99b6c5d62e56a445583fd4c08b (patch)
treef98fccc44829e3f52e585d6b41a1942aa52bd8b7 /wqflask/maintenance/generate_kinship_from_bimbam.py
parent7e49c006af9c4f7453c3578a7d4f1fc4d7bdf3ed (diff)
parent9e9e0e4d440383f617542e810a1115833eafd7bf (diff)
downloadgenenetwork2-c1a6ca69f7c48d99b6c5d62e56a445583fd4c08b.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno
Diffstat (limited to 'wqflask/maintenance/generate_kinship_from_bimbam.py')
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py30
1 files changed, 18 insertions, 12 deletions
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 60257b28..9f01d094 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -13,14 +13,17 @@ sys.path.append("..")
import os
import glob
-class GenerateKinshipMatrices(object):
+
+class GenerateKinshipMatrices:
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
+ 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)
@@ -33,9 +36,12 @@ class GenerateKinshipMatrices(object):
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)
+ 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:
@@ -46,15 +52,15 @@ class GenerateKinshipMatrices(object):
print(" Exception:", why)
print(traceback.print_exc())
print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
- convertob.latest_col_pos))
+ convertob.latest_col_pos))
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
-
-
-if __name__=="__main__":
+
+
+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
+
+ # ./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