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

[Dan Bolser]

2009/1/21 Scott Cain <scott at scottcain.net>:
> 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.

Thanks all for the info.

All the best,
Dan.



>
> 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.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> 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
>