[Bioperl-l] bp_genbank2gff3 and method "binomial" problem

Dave Messina David.Messina at sbc.su.se
Wed Jun 18 09:20:10 EDT 2008


Hi Luis,

This is the line that you're dying on:
my ($species)= $seq->annotation->get_Annotations("species")
||      ( $seq->can('species') ?
   $seq->species()->binomial() : undef );


So it looks like there might be a problem with the species field in one of
the Genbank entries.

Could you extract from your input file the record that it is choking on? We
need it to reproduce the error.

And then, to help us keep track of the problem, could you submit a copy of
that record and your description of what happened to our bug tracker?

http://bugzilla.open-bio.org/


Please be sure to indicate which version of BioPerl you are using. Line 674
in the current version of genbank2gff3.pl is a comment (the above is line
672), so I suspect you may be using an outdated version. The problem may
already have been fixed in the current version.

More instructions here if needed:
http://www.bioperl.org/wiki/Bugs


Thanks,
Dave


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