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-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py66
1 files changed, 0 insertions, 66 deletions
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
deleted file mode 100644
index 9f01d094..00000000
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/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:
- 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