I've been migrating most of my software/scripts over to GFF3, and have encountered a possible bug with Artemis (v11) on Linux x86_64.
When the GFF3 has multiple sequences in the ##FASTA section, Artemis dies with:
Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException:
uk.ac.sanger.artemis.io.EmblStreamFeature
at
uk.ac.sanger.artemis.io.GFFDocumentEntry.combineGeneFeatures(GFFDocumentEntry.java:166)
at
uk.ac.sanger.artemis.io.GFFDocumentEntry.<init>(GFFDocumentEntry.java:75)
However, if i REMOVE the >region00001 sequence so there is only the
one >Seq sequence, all is ok. The extra sequences in the ##FASTA
section are commonly used to store CDS translations, or when the GFF
covers lots of sequences eg. contigs in an assembly.
I have attached a .GFF3 file which causes this (and inlined it below
for completeness).
##gff-version 3
Seq vbc region 20 60 . + .
ID=region00001;product=Junk DNA
##FASTA
>Seq
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC
>region00001
GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATG
Thank you.
--
--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA
art_gff_multiple_seq_bug.gff3
Description: Binary data
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