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

Mark A. Jensen maj at fortinbras.us
Mon Jan 19 17:03:31 EST 2009

Lincoln- that's great- thanks- MAJ
  ----- Original Message ----- 
  From: Lincoln Stein 
  To: Mark A. Jensen 
  Cc: Dan Bolser ; bioperl-l at lists.open-bio.org 
  Sent: Monday, January 19, 2009 4:21 PM
  Subject: Re: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?

  Hi Mark,

  I've forwarded your bug report to the script's author.


  On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

    Well, Dan,

    You may get exactly what you need from the line of code you have written. Excellent!
    However, genbank files can be complex, and will contain information that users may
    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 least
    one person (the script's author) did.

    One way to discover 'extra benefits' is to examine the script documentation, which
    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 context,
    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 done,
    but only with a generality that would have been pointless overhead for my application.

    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,

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  Lincoln D. Stein

  Ontario Institute for Cancer Research
  101 College St., Suite 800
  Toronto, ON, Canada M5G0A3
  416 673-8514
  Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

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