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

[Scott Cain]

Hi Hilmar,

Yes, this is one of a few things the script does that the simple SeqIO
based transformation will likely not deal with well.  It also attempts
to standarize on Sequence Ontology terms and tries to deal with
various odd things that crop up in GenBank/EMBL files.

Scott


On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
> Doesn't this script attempt to unflatten the features too?
>
>        -hilmar
>
> 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,
>>
>> Dan.
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research