From 425f0e9d8977f8cf741f596315a56c91b750988a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 Sep 2017 16:13:42 +0000
Subject: Added the script to convert bimbam to kinship matrices

---
 .../maintenance/generate_kinship_from_bimbam.py    | 59 ++++++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 wqflask/maintenance/generate_kinship_from_bimbam.py

(limited to 'wqflask/maintenance/generate_kinship_from_bimbam.py')

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
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