diff options
Diffstat (limited to 'wqflask/maintenance/generate_kinship_from_bimbam.py')
| -rw-r--r-- | wqflask/maintenance/generate_kinship_from_bimbam.py | 31 |
1 files changed, 18 insertions, 13 deletions
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index b53f5dda..9f01d094 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -8,20 +8,22 @@ 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): + +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) @@ -34,9 +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: @@ -47,15 +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 \ No newline at end of file + + # ./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 |