[Bioperl-l] SeqIO; writing to custom out format?

[Brian Osborne]

Charles,

Do you mean you'd like to load your Genbank files into postgres? Do you 
need to use your own schema or can you use the biosql database? Are you 
simply going to discard the fasta files after? Excuse the many 
questions but the answers are slightly different depending on what you 
want to do.

Brian O.


On Friday, February 21, 2003, at 05:22 AM, Charles Hauser wrote:

> All,
>
> I think there is a clean way using SeqIO to write to a custom format,
> but am missing it.
>
> Parsing genbank files, I would like to write a modified fasta outfile
> which includes/or uses the gene name as the top line in lie of the
> default
> 	$name = format_name($feat->_tag_value('gene'));
>  to generate :
>
>> 'gene name'	'accession'
> seq	
>
>
> Or am I better off outputting a GFF file?
>
> I am going to be using these to load a database(postgres).
>
> regards,
>
> Chuck
>
>
> my %outfile = ('Cr' => {
>                         'Fasta' => Bio::SeqIO->new('-file' => '>Cr.fa',
>                                                    '-format' => 
> 'fasta')
>                        }
>                );
>
>
> FEATURES             Location/Qualifiers
>      source          1..5131
>                      /organism="Chlamydomonas reinhardtii"
>                      /strain="2137"
>                      /db_xref="taxon:3055"
>                      /dev_stage="vegetative"
>      gene            
> join(21..117,199..264,618..685,1031..1123,2513..2578,
>                      2892..3023,3355..3505,3906..4109,4383..4498)
>                      /gene="Pgp1"
>      CDS             
> join(21..117,199..264,618..685,1031..1123,2513..2578,
>                      2892..3023,3355..3505,3906..4109,4383..4498)
>                      /gene="Pgp1"
>                      /codon_start=1
>                      /product="phosphoglycolate phosphatase precursor"
>                      /protein_id="BAC56941.1"
>
>
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