Mercurial > repos > lldelisle > fromgtftobed12
changeset 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 | |
| files | fromgtfTobed12.py fromgtfTobed12.xml test-data/testWithGeneIds.bed |
| diffstat | 3 files changed, 126 insertions(+), 13 deletions(-) [+] |
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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)
--- a/fromgtfTobed12.xml Fri Nov 04 15:37:12 2022 +0000 +++ b/fromgtfTobed12.xml Fri Nov 03 14:13:51 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy0"> +<tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy1"> <description> Convert a gtf to a bed12.</description> <requirements> <requirement type="package" version="0.11.1">gffutils</requirement> @@ -14,7 +14,9 @@ <command> <![CDATA[ python3 $__tool_directory__/fromgtfTobed12.py - $useGene + #if str($preferedName) != "": + --preferedName $preferedName + #end if $mergeTranscripts $ucscformat --output $output @@ -23,12 +25,12 @@ </command> <inputs> <param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/> - <param argument="--useGene" type="boolean" checked="False" truevalue="--useGene" falsevalue="" label="Uses the gene name instead of the transcript name."/> <param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?"> <option value="" selected="true">No</option> <option value="--mergeTranscripts">Yes</option> <option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option> </param> + <param argument="--preferedName" type="text" value="" label="Use a specific name for the 4th column" help="By default the 4th column will be transcript_name or gene_name if you merge transcripts. If you prefer 'gene_id', for example, then set this option." /> <param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/> </inputs> @@ -45,20 +47,24 @@ <test> <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> <param name="ucscformat" value="--ucscformat"/> - <param name="useGene" value="--useGene"/> + <param name="preferedName" value="gene_name"/> <output name="output" file="testWithGenes.bed"/> </test> <test> <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> + <param name="ucscformat" value="--ucscformat"/> + <param name="preferedName" value="gene_id"/> + <output name="output" file="testWithGeneIds.bed"/> + </test> + <test> + <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> <param name="mergeTranscripts" value="--mergeTranscripts"/> - <param name="useGene" value="--useGene"/> <param name="ucscformat" value=""/> <output name="output" file="testMergeNotUCSC.bed"/> </test> <test> <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> <param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/> - <param name="useGene" value="--useGene"/> <param name="ucscformat" value=""/> <output name="output" file="testMergeExons.bed"/> </test>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testWithGeneIds.bed Fri Nov 03 14:13:51 2023 +0000 @@ -0,0 +1,105 @@ +chr1 11868 14409 ENSG00000223972 0 + 11868 11868 0 3 359,109,1189 0,744,1352 +chr1 12009 13670 ENSG00000223972 0 + 12009 12009 0 6 48,49,85,78,154,218 0,169,603,965,1211,1443 +chr1 14403 29570 ENSG00000227232 0 - 14403 14403 0 11 98,34,152,159,198,136,137,147,99,154,37 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130 +chr1 17368 17436 ENSG00000278267 0 - 17368 17368 0 1 68 0 +chr1 29553 31097 ENSG00000243485 0 + 29553 29553 0 3 486,104,122 0,1010,1422 +chr1 30266 31109 ENSG00000243485 0 + 30266 30266 0 2 401,134 0,709 +chr1 30365 30503 ENSG00000284332 0 + 30365 30365 0 1 138 0 +chr1 34553 36081 ENSG00000237613 0 - 34553 34553 0 3 621,205,361 0,723,1167 +chr1 35244 36073 ENSG00000237613 0 - 35244 35244 0 2 237,353 0,476 +chr1 52472 53312 ENSG00000268020 0 + 52472 52472 0 1 840 0 +chr1 57597 64116 ENSG00000240361 0 + 57597 57597 0 3 56,157,1201 0,1102,5318 +chr1 62948 63887 ENSG00000240361 0 + 62948 62948 0 1 939 0 +chr1 65418 71585 ENSG00000186092 0 + 65564 70005 0 3 15,54,2549 0,101,3618 +chr1 69054 70108 ENSG00000186092 0 + 69090 70005 0 1 1054 0 +chr1 89294 120932 ENSG00000238009 0 - 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