57 lines
1.2 KiB
Python
57 lines
1.2 KiB
Python
#!/usr/bin/env python3
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import os
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import sys
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import subprocess
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import math
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from sv_modules import *
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print("--------------------------------------------\n")
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print("HLA-B Variant Analysis with StellarPGx\n")
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print("--------------------------------------------\n")
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infile = sys.argv[1]
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cov_file = sys.argv[2]
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def get_core_variants(infile, cn):
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core_vars = []
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for line in open(infile, "r"):
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line = line.strip()
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core_vars.append(line)
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core_vars = ";".join(sorted(core_vars))
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if int(cn) == 1:
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core_vars = core_vars.replace("~0/1", "~1/1")
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if os.stat(infile).st_size == 0:
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core_vars = "No core SNVs detected; haplotypes equivalent to GRCh38 content"
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return core_vars
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cn = get_total_CN(cov_file)[0]
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av_ctrl_cov = get_total_CN(cov_file)[2]
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exon_cov = get_total_CN(cov_file)[3]
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print("Initially computed Copy Number = {}".format(cn))
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for i in range(1, len(exon_cov)):
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if exon_cov[i-1]/av_ctrl_cov < 0.45 :
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print ('Check exon {} for potential deletion if using high coverage WGS'.format(str(i)))
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else:
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pass
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supp_core_vars = get_core_variants(infile, cn)
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print("\nSample core variants:")
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print(supp_core_vars)
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