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Creating gff from genePred returns error
I was trying to create custom miso annotation using these instructions but got the following error:
python /local/data/home/adomingu/env/lib/python2.7/site-packages/rnaseqlib/gff/gff_make_annotation.py ./ ./gff --flanking-rule commonshortest --genome-label Zv9.junker
Making GFF alternative events annotation...
- UCSC tables read from: /fsimb/groups/imb-kettinggr/genomes/Danio_rerio/Ensembl/Zv9/Annotation/Archives/archive-2014-05-23-16-02-26/Genes/miso
- Output dir: /fsimb/groups/imb-kettinggr/genomes/Danio_rerio/Ensembl/Zv9/Annotation/Archives/archive-2014-05-23-16-02-26/Genes/miso/gff
Loaded 1 UCSC tables.
Loading tables...
Traceback (most recent call last):
File "/local/data/home/adomingu/env/lib/python2.7/site-packages/rnaseqlib/gff/gff_make_annotation.py", line 65, in <module>
main()
File "/local/data/home/adomingu/env/lib/python2.7/site-packages/rnaseqlib/gff/gff_make_annotation.py", line 61, in main
make_annotation(args)
File "/local/data/home/adomingu/env/lib/python2.7/site-packages/rnaseqlib/gff/gff_make_annotation.py", line 35, in make_annotation
sanitize=args.sanitize)
File "/local/data/home/adomingu/env/local/lib/python2.7/site-packages/rnaseqlib/events/defineEvents.py", line 933, in defineAllSplicing
sg = splicegraph.SpliceGraph(table_fnames)
File "/local/data/home/adomingu/env/local/lib/python2.7/site-packages/rnaseqlib/events/SpliceGraph.py", line 446, in __init__
self.load_tables()
File "/local/data/home/adomingu/env/local/lib/python2.7/site-packages/rnaseqlib/events/SpliceGraph.py", line 496, in load_tables
self.tables[table_label] = parseTables.readTable(table_fname)
File "/local/data/home/adomingu/env/local/lib/python2.7/site-packages/rnaseqlib/events/parseTables.py", line 56, in readTable
for col_num in range(len(header))])
IndexError: list index out of range
Since was converting GTF to genePred using gtfToGenePred -genePredExt gtf genepred
and the output was not exactly the same as represented in rnaseqlib's intructions:
gtfToGenePred -genePredExt Danio_rerio.Zv9.74.ImprovedUTRs.Junker_et_al_2014.noZv.so.gtf ensGene.txt
head ensGene.txt
ENSDART00000152494 chr1 - 2286 4806 4806 4806 2 2286,4578, 2340,4806, 0 ENSDARG00000096573 none none -1,-1,
ENSDART00000152276 chr1 + 3799 15148 15148 15148 8 3799,4645,5177,5532,6246,9049,9239,13072, 3930,4809,5202,5646,6393,9141,9360,15148, 0 ENSDARG00000076045 none none -1,-1,-1,-1,-1,-1,-1,-1,
ENSDART00000109479 chr1 + 3799 15138 15138 15138 9 3799,4645,5177,5532,6246,11049,11239,13072,14304, 3930,4809,5202,5646,6393,11141,11360,13958,15138, 0 ENSDARG00000076045 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,
I tested it further using (i) the ensGene track from UCSC downloaded for both Zv9 and hg19; (ii) a file with the example genePred in the help page. All failed with the same message.
I have no idea of what the problem is.