removed pgx-main

pgx-main/scripts/cyp4f2/b37/bin/stellarpgx.py

@@ -1,72 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-import subprocess
-from snv_def_modules import *
-from bkg_modules import *
-
-
-print("--------------------------------------------\n")
-
-print("CYP4F2 Star Allele Calling with StellarPGx\n")
-
-print("--------------------------------------------\n")
-
-
-
-database = sys.argv[1]
-infile = sys.argv[2]
-infile_full = sys.argv[3]
-infile_full_gt = sys.argv[4]
-infile_spec = sys.argv[5]
-
-
-cn = 2
-
-
-supp_core_vars = get_core_variants(infile, cn)
-
-print("\nSample core variants:")
-print(supp_core_vars)
-
-
-snv_def_calls = cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infile_spec, cn)
-
-if snv_def_calls == None:
-
-    bac_alleles = get_backgroud_alleles(database, supp_core_vars)
-
-    if bac_alleles == None:
-        print("\nResult:")
-        print("Possible novel allele or suballele present: interpret with caution")
-
-
-    else:
-        print("\nCandidate alleles:")
-        print("[" + bac_alleles[-1] + "]")
-
-        print("\nResult:")
-        print("Possible novel allele or suballele present: interpret with caution; experimental validation and expert review through PharmVar is recommended")
-        print("\nLikely background alleles:")
-        print("[" + bac_alleles[0] + "]")
-
-    sys.exit()
-
-
-
-else:
-    snv_cand_alleles = snv_def_calls[0]
-    snv_def_alleles = snv_def_calls[-1]
-
-
-print("\nCandidate alleles:")
-print(snv_cand_alleles)
-
-
-dip_variants = get_all_vars_gt(infile_full_gt)
-
-
-print("\nResult:")
-
-print(snv_def_alleles)