[Bioperl-l] Genbank parsers

[Ewan Birney]

On Wed, 27 Mar 2002, Rhazes Spell wrote:

> > You can tell my laziness from this question.  Could someone suggest a good
> > parser to take CDS sequences from genbank formatted files. (The *.gbff file
> > from NCBI FTP site).  If the output file is FASTA, it would be great.
> 
> In addition, could someone one recommend a parser (or bioPerl module) that
> can parse the features out of the GenBank format?

$seqio = Bio::SeqIO->new( -format => 'genbank', -file => 'myfile');

while( $seq  = $seqio->next_seq ) {
   # do something with $seq
}


> 
> Thanks!
> 
> 
> **************************************
> Duke University
> Department of Biomedical Engineering
> Duke University Medical Center,
>  Center for Genome Technology
> 
> rhazes.spell@duke.edu
> 919.684.2720
> ***************************************
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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