[Biojava-l] GCG format...

[Wiepert, Mathieu]

Hi,

Have you considered doing a system call to seqret (from emboss)?  Is that a possibility for you?  Not sure what system you are running on, etc.  May be a hack, but it would work.  Or else system calls to GCG, which will also do some formatting for you.  Again a hack, but workable...

-Mat

> -----Original Message-----
> From: Andrew Macgregor [mailto:andrew@anatomy.otago.ac.nz]
> Sent: Thursday, October 10, 2002 10:58 PM
> To: BioJava
> Subject: [Biojava-l] GCG format...
> 
> 
> Hi all,
> 
> I see from the mailing list archive that there was mention of someone
> creating a GCG format for BioJava. Did this happen? Is it 
> necessary? I'm
> interested in seeing how to convert from one format to 
> another a bit like I
> could with this bioperl script. Is something like this 
> possible. I can see
> how to use Embl, Genbank and Fasta but not GCG.
> 
> TIA for any pointers.
> 
> 
> use Bio::SeqIO;
> 
> my $in  = Bio::SeqIO->new(-file => "$ARGV[0]" , '-format' => 'Fasta');
> 
> # number for files
> my $i=1;
> 
> while ( my $seq = $in->next_seq() ) {
> 
>     my $out = Bio::SeqIO->new(-file => ">$i.seq" , '-format' 
> => 'gcg');
>     $out->write_seq($seq);
> 
>     $i++;
> }
> 
> 
> Cheers, Andrew.
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>