Mercurial > repos > mheinzl > variant_analyzer2

comparison mut2sscs.py @ 10:e18c5293aac7 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 Thu, 04 Feb 2021 09:01:43 +0000
parents ced1a529e7cd
children 84a1a3f70407
comparison
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9:5800e3acb06d 10:e18c5293aac7
66 for variant in VCF(file1): 66 for variant in VCF(file1):
67 chrom = variant.CHROM 67 chrom = variant.CHROM
68 stop_pos = variant.start 68 stop_pos = variant.start
69 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) 69 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
70 ref = variant.REF 70 ref = variant.REF
71 if len(variant.ALT) > 0: 71 if len(variant.ALT) == 0:
72 continue
73 else:
72 alt = variant.ALT[0] 74 alt = variant.ALT[0]
73 else:
74 alt = variant.ALT
75 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt 75 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
76 76
77 if len(ref) == len(alt): 77 if len(ref) == len(alt):
78 78
79 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): 79 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000):