continue
os.chdir("alignment_LAN210_v0.9m")
mutations = CollectionVCF(vcf_file=sample + suffix,
from_file=True)
print("Totaly %s mutations" % len(mutations))
mutations.test_thresholds(extracting_method='distance', threshold=(50, 5000, 100),
testing_dir="testing_threshold")
"""
sample_set_names_list = [
"PmCDA1_3d", "HAP", "PmCDA1_sub1_3d", "PmCDA1_6d", "HAP_sub1",
"PmCDA1_sub1_6d", "A1_3d", "A1_6d", "A3G_3d", "AID_3d", "AID_6d"
]
suffix = "_SNP.vcf"
workdir = "/media/mahajrod/d9e6e5ee-1bf7-4dba-934e-3f898d9611c8/Data/LAN2xx/combined_vcf/test_thresholds/"
sample_dir = "/media/mahajrod/d9e6e5ee-1bf7-4dba-934e-3f898d9611c8/Data/LAN2xx/combined_vcf/SNP_annotated_raw_vcf/"
for sample_set in sample_set_names_list:
print("Handling %s" % sample_set)
os.chdir(workdir)
os.system("mkdir -p %s" % sample_set)
os.chdir(sample_set)
mutations = CollectionVCF(vcf_file=sample_dir + sample_set + suffix,
from_file=True)
print("Totaly %s mutations" % len(mutations))
mutations.test_thresholds(extracting_method='distance',
threshold=(50, 5000, 100),
testing_dir="testing_threshold")
__author__ = 'mahajrod'
import os
from Parsers.VCF import CollectionVCF
if __name__ == "__main__":
workdir = "/media/mahajrod/d9e6e5ee-1bf7-4dba-934e-3f898d9611c8/Data/LAN2xx/all"
os.chdir(workdir)
samples_list = sorted(os.listdir("."))
suffix = "_GATK_best_merged.vcf"
for sample in samples_list:
print("Handling %s" % sample)
os.chdir(workdir)
os.chdir(sample)
if "alignment_LAN210_v0.9m" not in os.listdir("."):
continue
os.chdir("alignment_LAN210_v0.9m")
mutations = CollectionVCF(vcf_file=sample + suffix, from_file=True)
print("Totaly %s mutations" % len(mutations))
mutations.test_thresholds(save_clustering=True,
testing_dir="testing_theshold_inconsistent")