[Bioperl-l] What's the best way to produce gff files from genebank/embl formats?

Brian Osborne bosborne11 at verizon.net
Thu Nov 15 14:19:41 EST 2007


Chris,

There's also a genbank2gff3.PLS script in the GMOD package (
http://gmod.cvs.sourceforge.net/gmod/schema/chado/load/bin/genbank2gff3.PLS?
revision=1.5&view=markup). However, it has not been modified for a couple of
years, it may not be the "preferred" script.

See http://gmod.org/wiki/index.php/Load_GenBank_into_Chado and
http://gmod.org/wiki/index.php/Load_RefSeq_Into_Chado for more information
on using Bioperl's bp_genbank2gff3 script.

Brian O.


On 11/15/07 1:43 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:

> There are currently many ways to get what you want, but not all are
> consistent (particularly re: GFF3).  We are aiming for more
> consistent, compliant GFF/GTF output in the next developer series
> (1.7) of Bioperl.
> 
> You can try using bp_genbank2gff or bp_genbank2gff3 (both in the
> scripts directory); these are probably the most common way when
> working directly from a seq record.  Bio::Tools::GFF is the most
> commonly used class though I'm unsure of it's status for GFF3
> output.  From within a Bio::SeqI you can call write_gff() (currently
> not very flexible) or from the SeqFeature itself gff_string().
> Bio::Graphics::Feature has the additional method gff3_string().
> Bio::FeatureIO is also an option, though I would consider it very
> experimental (it will likely undergo significant revision in the next
> bioperl dev series).
> 
> Any others anyone can think of, maybe non-BioPerl related as well?
> 
> chris
> 
> On Nov 15, 2007, at 9:44 AM, Lucia Peixoto wrote:
> 
>> Hi
>> I was asked this question recently
>> and it occurred to me I must be doing things inefficiently
>> To produce gff file I was using SeqIO to parse the required fields,
>> then
>> according to the conventions just printing out whatever was
>> required tab
>> delimited, which is easy
>> 
>> but if I wanted to generate a genbank file, extracting features
>> from a gff file
>> and a plain fasta file it was more complicated
>> is there support for gff in bioperl now?
>> anyone can contribute with  smart way to go from/to gff, genebank
>> and embl?
>> 
>> thanks very much
>> 
>> Lucia Peixoto
>> Department of Biology,SAS
>> University of Pennsylvania
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> 
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