Mercurial > repos > fubar > jbrowse2dev
diff jbrowse2/blastxml_to_gapped_gff3.py @ 7:234cf4490901 draft
Uploaded
author | fubar |
---|---|
date | Fri, 05 Jan 2024 04:31:35 +0000 |
parents | 88b9b105c09b |
children |
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--- a/jbrowse2/blastxml_to_gapped_gff3.py Fri Jan 05 01:58:02 2024 +0000 +++ b/jbrowse2/blastxml_to_gapped_gff3.py Fri Jan 05 04:31:35 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:]