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

Mark A. Jensen maj at fortinbras.us
Mon Jan 19 15:04:53 UTC 2009

Well, Dan,

You may get exactly what you need from the line of code you have written. 
However, genbank files can be complex, and will contain information that users 
want to manipulate in different ways, particularly in ways that are computable.
This script has other features under the hood, that you may not require, but at 
one person (the script's author) did.

One way to discover 'extra benefits' is to examine the script documentation, 
describes in detail the capabilities of the script. To access it, open the 
script file,
or use another possibly superfluous script that parses files in a particular 
called "perldoc", like this:
perldoc genbank2gff3.PLS

It's also worth keeping in mind that BioPerl, as heavily object-oriented as it 
is, is
written to optimize development time, maybe at the expense of CPU cycles or
disk space. I have written my own modules that BioPerl could certainly have 
but only with a generality that would have been pointless overhead for my 

I can have a look at the error.
----- Original Message ----- 
From: "Dan Bolser" <dan.bolser at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Monday, January 19, 2009 9:44 AM
Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?

>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,
> Dan.
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