72 lines
1.4 KiB
Python
72 lines
1.4 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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from snv_def_modules import *
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from bkg_modules import *
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print("--------------------------------------------\n")
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print("CYP1A2 Star Allele Calling with StellarPGx\n")
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print("--------------------------------------------\n")
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database = sys.argv[1]
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infile = sys.argv[2]
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infile_full = sys.argv[3]
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infile_full_gt = sys.argv[4]
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infile_spec = sys.argv[5]
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cn = 2
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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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snv_def_calls = cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infile_spec, cn)
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if snv_def_calls == None:
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bac_alleles = get_backgroud_alleles(database, supp_core_vars)
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if bac_alleles == None:
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print("\nResult:")
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print("Possible novel allele or suballele present: interpret with caution")
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else:
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print("\nCandidate alleles:")
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print("[" + bac_alleles[-1] + "]")
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print("\nResult:")
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print("Possible novel allele or suballele present: interpret with caution; experimental validation and expert review through PharmVar is recommended")
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print("\nLikely background alleles:")
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print("[" + bac_alleles[0] + "]")
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sys.exit()
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snv_cand_alleles = snv_def_calls[0]
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print("\nCandidate alleles:")
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print(snv_cand_alleles)
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snv_def_alleles = snv_def_calls[-1]
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dip_variants = get_all_vars_gt(infile_full_gt)
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print("\nResult:")
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print(snv_def_alleles)
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