[Biojava-l] GCG format...

[Schreiber, Mark]

One of the issues with GCG format is the checksum. I have seen methods
that calculate and verify the checksum but I'm not sure that they are
supposed to be used. Ie GCG won't tell you how to do it so doing it
anyway might be breaking some annoying little copyright law.

- Mark


> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu] 
> Sent: Saturday, 12 October 2002 4:54 a.m.
> To: 'Andrew Macgregor'; BioJava
> Subject: RE: [Biojava-l] GCG format...
> 
> 
> 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
> > 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================