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authorzsloan2017-09-07 16:13:42 +0000
committerzsloan2017-09-07 16:13:42 +0000
commit425f0e9d8977f8cf741f596315a56c91b750988a (patch)
treebb86d110ac893ac4ffaa8b088eee05c6179c7f9f
parent76e1810abb05457a4c38c8fcebce334f5d1493bf (diff)
downloadgenenetwork2-425f0e9d8977f8cf741f596315a56c91b750988a.tar.gz
Added the script to convert bimbam to kinship matrices
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py59
1 files changed, 59 insertions, 0 deletions
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
new file mode 100644
index 00000000..f322341d
--- /dev/null
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -0,0 +1,59 @@
+#!/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
+
+"""
+
+from __future__ import print_function, division, absolute_import
+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])
+ 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 = """/home/zas1024/genotype_files/genotype/"""
+ Bimbam_Directory = """/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 \ No newline at end of file