[Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?

Dan Bolser dan.bolser at gmail.com
Mon Jan 19 14:44:40 UTC 2009

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,


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