Mercurial > repos > mheinzl > variant_analyzer2
changeset 10:e18c5293aac7 draft
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 | 5800e3acb06d |
| children | 84a1a3f70407 |
| files | mut2read.py mut2sscs.py read2mut.py |
| diffstat | 3 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/mut2read.py Thu Feb 04 08:57:57 2021 +0000 +++ b/mut2read.py Thu Feb 04 09:01:43 2021 +0000 @@ -74,10 +74,10 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - if len(variant.ALT) > 0: + if len(variant.ALT) == 0: + continue + else: alt = variant.ALT[0] - else: - alt = variant.ALT print(alt) chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
--- a/mut2sscs.py Thu Feb 04 08:57:57 2021 +0000 +++ b/mut2sscs.py Thu Feb 04 09:01:43 2021 +0000 @@ -68,10 +68,10 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - if len(variant.ALT) > 0: + if len(variant.ALT) == 0: + continue + else: alt = variant.ALT[0] - else: - alt = variant.ALT chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt if len(ref) == len(alt):
--- a/read2mut.py Thu Feb 04 08:57:57 2021 +0000 +++ b/read2mut.py Thu Feb 04 09:01:43 2021 +0000 @@ -132,10 +132,10 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - if len(variant.ALT) > 0: + if len(variant.ALT) == 0: + continue + else: alt = variant.ALT[0] - else: - alt = variant.ALT chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt if len(ref) == len(alt):