Mercurial > repos > mheinzl > variant_analyzer2

comparison mut2read.py @ 75:6ccff403db8a draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Tue, 23 Mar 2021 15:18:17 +0000
parents d21960b45a6b
children fdfe9a919ff7
comparison
equal deleted inserted replaced
74:5023186c2061 75:6ccff403db8a
70 cvrg_dict = {} 70 cvrg_dict = {}
71 71
72 for variant in VCF(file1): 72 for variant in VCF(file1):
73 chrom = variant.CHROM 73 chrom = variant.CHROM
74 stop_pos = variant.start 74 stop_pos = variant.start
75 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
76 ref = variant.REF 75 ref = variant.REF
77 if len(variant.ALT) == 0: 76 if len(variant.ALT) == 0:
78 continue 77 continue
79 else: 78 else:
80 alt = variant.ALT[0] 79 alt = variant.ALT[0]
81 print(alt)
82 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt 80 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
83
84
85 dcs_len = [] 81 dcs_len = []
86 if len(ref) == len(alt): 82 if len(ref) == len(alt):
87 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000): 83 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000):
88 if pileupcolumn.reference_pos == stop_pos: 84 if pileupcolumn.reference_pos == stop_pos:
89 count_alt = 0 85 count_alt = 0
150 out.write(curr_qual + "\n") 146 out.write(curr_qual + "\n")
151 147
152 148
153 if __name__ == '__main__': 149 if __name__ == '__main__':
154 sys.exit(mut2read(sys.argv)) 150 sys.exit(mut2read(sys.argv))
155