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Victorian-Bioinformatics-Consortium / degust

Deprecated : Use https://github.com/drpowell/degust
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convert_models.py script failed on Ensembl gff3 file #14

Closed lmanchon closed 10 years ago

lmanchon commented 10 years ago

--Hi,

recently i have used convert_models.py script to convert gff3 file to gtf as: ./convert_models.py Strongylocentrotus_purpuratus.gff3 --gtf=GTF

and it returns errors: Loading gene models from Strongylocentrotus_purpuratus.gff3 Traceback (most recent call last): File "/save/dpiquemal/SPLICEGRAPHER/bin/convert_models.py", line 48, in model = loadGeneModels(inputFile, verbose=opts.verbose, alltypes=True) File "/save/dpiquemal/SPLICEGRAPHER/lib/python/SpliceGrapher/formats/loader.py", line 32, in loadGeneModels return GeneModel(path, _args) File "/save/dpiquemal/SPLICEGRAPHER/lib/python/SpliceGrapher/formats/GeneModel.py", line 938, in init self.loadGeneModel(gffPath, _args) File "/save/dpiquemal/SPLICEGRAPHER/lib/python/SpliceGrapher/formats/GeneModel.py", line 1476, in loadGeneModel (lineCtr, recType, chrName, ','.join(self.mRNAforms.keys()))) File "/save/dpiquemal/SPLICEGRAPHER/lib/python/SpliceGrapher/formats/GeneModel.py", line 1270, in conditionalException if not ignoreErrors : raise Exception(s) Exception: line 4310: cds has unrecognized chromosome: scaffold14395 (known: )

my gff3 input file is available here: ftp://ftp.ensemblgenomes.org/pub/metazoa/release-22/gff3/strongylocentrotus_purpuratus/Strongylocentrotus_purpuratus.GCA_000002235.2.22.gff3.gz

Laurent --

drpowell commented 10 years ago

This doesn't have anything to do with degust.