diff options
Diffstat (limited to 'wqflask/maintenance/convert_geno_to_bimbam.py')
| -rw-r--r-- | wqflask/maintenance/convert_geno_to_bimbam.py | 8 |
1 files changed, 6 insertions, 2 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 45522705..528b98cf 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -140,6 +140,8 @@ class ConvertGenoFile(object): key, _separater, value = row.partition(':') key = key.strip() value = value.strip() + if key == "@filler": + raise EmptyConfigurations if key in self.haplotype_notation: self.configurations[value] = self.haplotype_notation[key] continue @@ -154,6 +156,8 @@ class ConvertGenoFile(object): if not input_file.endswith(('geno', '.geno.gz')): continue group_name = ".".join(input_file.split('.')[:-1]) + if group_name == "HSNIH-Palmer": + continue geno_output_file = os.path.join(new_directory, group_name + "_geno.txt") pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt") snp_output_file = os.path.join(new_directory, group_name + "_snps.txt") @@ -176,8 +180,8 @@ class ConvertGenoFile(object): break if __name__=="__main__": - Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/""" - New_Geno_Directory = """/home/zas1024/genotype_files/genotype/bimbam/""" + Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" + New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam""" #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno""" #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") |