Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 10:e18c5293aac7 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Thu, 04 Feb 2021 09:01:43 +0000 |
parents | ced1a529e7cd |
children | 84a1a3f70407 |
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9:5800e3acb06d | 10:e18c5293aac7 |
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130 # break | 130 # break |
131 chrom = variant.CHROM | 131 chrom = variant.CHROM |
132 stop_pos = variant.start | 132 stop_pos = variant.start |
133 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) | 133 #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) |
134 ref = variant.REF | 134 ref = variant.REF |
135 if len(variant.ALT) > 0: | 135 if len(variant.ALT) == 0: |
136 continue | |
137 else: | |
136 alt = variant.ALT[0] | 138 alt = variant.ALT[0] |
137 else: | |
138 alt = variant.ALT | |
139 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt | 139 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt |
140 | 140 |
141 if len(ref) == len(alt): | 141 if len(ref) == len(alt): |
142 mut_array.append([chrom, stop_pos, ref, alt]) | 142 mut_array.append([chrom, stop_pos, ref, alt]) |
143 i += 1 | 143 i += 1 |