[Bioperl-l] Re: [Bioperl-guts-l] tigr to genbank

[Jason Stajich]

Not much in there really fits into the concept of a genbank file.  There
is no sequence, the rest of the fields I guess you want them to be stored
as DBlinks or annotations?

If you can map the pieces you want to keep into a seq object you just put
them in and then write out the sequence.

I'll do the easy one, accession:
use Bio::SeqIO;
use Bio::Seq;
my $seq = Bio::Seq->new();
my $out = Bio::SeqIO->new(-format => 'genbank');
$seq->accession_number($accession);
$out->write_seq($seq);

-jason
On Mon, 21 Jun 2004, Jinal Jhaveri wrote:

> TIGR Locus,TIGR Common Name,TIGR Gene Symbol,TIGR Enzyme Commission #,Primary
> Locus,Primary Common Name,Primary Gene Symbol,Primary Enzyme Commission #,Pri
> mary Annotation Comment,Primary 5' End,Primary Sequence Length,Primary Protein
> Length,TIGR 5' End,TIGR 3' End,TIGR Sequence Length,TIGR Protein Length,Main
> role,Subrole,SWISS-PROT/TrEMBL Accession,GenBank ID,TIGR MW,TIGR PI,TIGR
> GC,Kingdom,Family,Organism Name,DNA molecule,GO Term
>
> NT02AT0001,conserved hypothetical protein,,,Atu0001,conserved hypothetical
> protein,,,product=conserved hypothetical protein note=identified by sequence
> sim
> ilarity; putative; ORF located using
> Blastx/Glimmer,203,822,273,266,1024,759,,Hypothetical
> proteins,Conserved,,,27885.89,7.0437,58.62,Bacteria,Proteobacter
> ia,Agrobacterium tumefaciens C58 UWash,Circular chromosome A.tumefaciens C58
> UWash,
>
> ......................
>
>
>
> I am sending you the header and one of the entries.
>
> thanks
> --Jinal
>
> On Monday 21 June 2004 02:34 pm, you wrote:
> > Can you show what the format looks like?
> >
> > On Mon, 21 Jun 2004, Jinal Jhaveri wrote:
> > > Can any one give me directions onto how I can convert the tab-formatted
> > > tigr data to genbank formatted data? Does this type of script exists?
> > >
> > >
> > > thanks
> > > --Jinal
> > > _______________________________________________
> > > Bioperl-guts-l mailing list
> > > Bioperl-guts-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu