[Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?
hlapp at gmx.net
Mon Jan 19 21:39:12 UTC 2009
Doesn't this script attempt to unflatten the features too?
On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote:
> I found the script 'bp_genbank2gff3.pl' gave an error and died while
> trying to convert a .emb into GFF format.
> head ~/perl5/bin/bp_genbank2gff3.pl
> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $;
> bp_genbank2gff3.pl --format embl my.emb
> Can't call method "binomial" on an undefined value at
> ~/perl5/bin/bp_genbank2gff3.pl line 690, <FH> line 347337.
> However, looking at the docs, I came up with this:
> perl -MBio::SeqIO -e '
> $s = Bio::SeqIO->new( -file => shift )->next_seq;
> print "# ", $s->feature_count, "\n";
> print $_->gff_string, "\n" foreach $s->get_SeqFeatures
> ' my.emb > my.emb.gff
> How come the BioPerl script is >1000 lines, and apparently the
> conversion only requires 1? What extra benefit would I get from using
> bp_genbank2gff3.pl (assuming it ran)?
> Thanks for any feedback,
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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