Mercurial > repos > fubar > jbrowse2
diff blastxml_to_gapped_gff3.py @ 17:4c201a3d4755 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
| author | fubar |
|---|---|
| date | Sun, 28 Jan 2024 06:48:52 +0000 |
| parents | d78175596286 |
| children | b1260bca5fdc |
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--- a/blastxml_to_gapped_gff3.py Thu Jan 25 07:58:28 2024 +0000 +++ b/blastxml_to_gapped_gff3.py Sun Jan 28 06:48:52 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:] @@ -290,7 +290,9 @@ help="Trim blast hits to be only as long as the parent feature", ) parser.add_argument( - "--trim_end", action="store_true", help="Cut blast results off at end of gene" + "--trim_end", + action="store_true", + help="Cut blast results off at end of gene", ) parser.add_argument("--include_seq", action="store_true", help="Include sequence") args = parser.parse_args()