Mercurial > repos > lldelisle > fromgtftobed12
diff fromgtfTobed12.py @ 1:6fd4b3b90220 draft default tip
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 15b8c2cc83708044413a152322bcbfca8a74d29a
| author | lldelisle |
|---|---|
| date | Fri, 03 Nov 2023 14:13:51 +0000 |
| parents | 418e4d0fe0bd |
| children |
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--- a/fromgtfTobed12.py Fri Nov 04 15:37:12 2022 +0000 +++ b/fromgtfTobed12.py Fri Nov 03 14:13:51 2023 +0000 @@ -23,13 +23,16 @@ "database creation") -def convert_gtf_to_bed(fn, fo, useGene, mergeTranscripts, +def convert_gtf_to_bed(fn, fo, preferedName, mergeTranscripts, mergeTranscriptsAndOverlappingExons, ucsc): db = gffutils.create_db(fn, ':memory:') # For each transcript: - prefered_name = "transcript_name" - if useGene or mergeTranscripts or mergeTranscriptsAndOverlappingExons: + if preferedName is not None: + prefered_name = preferedName + elif mergeTranscripts or mergeTranscriptsAndOverlappingExons: prefered_name = "gene_name" + else: + prefered_name = "transcript_name" if mergeTranscripts or mergeTranscriptsAndOverlappingExons: all_items = db.features_of_type("gene", order_by='start') else: @@ -127,12 +130,11 @@ argp.add_argument('--output', default=sys.stdout, type=argparse.FileType('w'), help="Output bed12 file.") -argp.add_argument('--useGene', action="store_true", - help="Use the gene name instead of the " - "transcript name.") argp.add_argument('--ucscformat', action="store_true", help="If you want that all chromosome names " "begin with 'chr'.") +argp.add_argument('--preferedName', default=None, + help="Name to use for bed output.") group = argp.add_mutually_exclusive_group() group.add_argument('--mergeTranscripts', action="store_true", help="Merge all transcripts into a single " @@ -144,7 +146,7 @@ " overlapping exons.") args = argp.parse_args() -convert_gtf_to_bed(args.input, args.output, args.useGene, +convert_gtf_to_bed(args.input, args.output, args.preferedName, args.mergeTranscripts, args.mergeTranscriptsAndOverlappingExons, args.ucscformat)