Mercurial > repos > fubar > jbrowse2
diff blastxml_to_gapped_gff3.py @ 98:b1260bca5fdc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
| author | bgruening |
|---|---|
| date | Wed, 05 Jun 2024 10:00:07 +0000 |
| parents | 4c201a3d4755 |
| children |
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--- a/blastxml_to_gapped_gff3.py Sat Jun 01 05:37:13 2024 +0000 +++ b/blastxml_to_gapped_gff3.py Wed Jun 05 10:00:07 2024 +0000 @@ -32,7 +32,7 @@ recid = record.query if " " in recid: - recid = recid[0 : recid.index(" ")] + recid = recid[0: recid.index(" ")] rec = SeqRecord(Seq("ACTG"), id=recid) for idx_hit, hit in enumerate(record.alignments): @@ -72,7 +72,7 @@ qualifiers["blast_" + prop] = getattr(hsp, prop, None) desc = hit.title.split(" >")[0] - qualifiers["description"] = desc[desc.index(" ") :] + qualifiers["description"] = desc[desc.index(" "):] # This required a fair bit of sketching out/match to figure out # the first time. @@ -161,9 +161,9 @@ fm = "" fs = "" for position in re.finditer("-", query): - fq += query[prev : position.start()] - fm += match[prev : position.start()] - fs += subject[prev : position.start()] + fq += query[prev: position.start()] + fm += match[prev: position.start()] + fs += subject[prev: position.start()] prev = position.start() + 1 fq += query[prev:] fm += match[prev:]