Hi Torsten
Thanks for that. I have fixed that and I hope to get that in the development
version in the next few days.
However, there is still a problem that has been mentioned before on the list
in that Artemis does not yet take into account column 1 in GFF3 (the ID of
the landmark used to establish the coordinate system). This means feature
positions that are not on the first sequence are wrong. I hope to get this
fixed soon as well.
Regards
Tim
On 3/11/09 12:28 AM, Torsten Seemann
torsten.seem...@infotech.monash.edu.au wrote:
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 region1 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=region1;product=Junk DNA
##FASTA
Seq
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT
GC
region1
GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATG
Thank you.
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