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

[Lincoln Stein]

Hi Mark,

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

Lincoln

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.
> Best,
> Mark
> ----- 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.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
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>