Mercurial > repos > mheinzl > variant_analyzer2
changeset 8:ced1a529e7cd 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 08:55:35 +0000 |
| parents | ded0dc6a20d3 |
| children | 5800e3acb06d |
| files | mut2read.py mut2sscs.py read2mut.py |
| diffstat | 3 files changed, 12 insertions(+), 4 deletions(-) [+] |
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--- a/mut2read.py Mon Jan 25 13:21:55 2021 +0000 +++ b/mut2read.py Thu Feb 04 08:55:35 2021 +0000 @@ -74,14 +74,16 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - alt = variant.ALT[0] + if len(variant.ALT) > 0: + alt = variant.ALT[0] + else: + alt = variant.ALT chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt dcs_len = [] if len(ref) == len(alt): for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000): - if pileupcolumn.reference_pos == stop_pos: count_alt = 0 count_ref = 0
--- a/mut2sscs.py Mon Jan 25 13:21:55 2021 +0000 +++ b/mut2sscs.py Thu Feb 04 08:55:35 2021 +0000 @@ -68,7 +68,10 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - alt = variant.ALT[0] + if len(variant.ALT) > 0: + 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 Mon Jan 25 13:21:55 2021 +0000 +++ b/read2mut.py Thu Feb 04 08:55:35 2021 +0000 @@ -132,7 +132,10 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - alt = variant.ALT[0] + if len(variant.ALT) > 0: + alt = variant.ALT[0] + else: + alt = variant.ALT chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt if len(ref) == len(alt):