[Bioperl-l] newbie needs help with "preferred_id_type"

[Andrew Walsh]

Hello,

I believe that if you set the display_id (or desc?) attribute to be the 
accession, you will get only the accession in the fasta header.

   while ( $seq = $in->next_seq() ) {
     print $seq->accession,"\n";

     $seq->display_id($seq->accession);
     # or ?
     $seq->desc($seq->accession);

     $out->write_seq($seq);
   }

One of those 2 should do the trick.

Andrew

Jonathan Miller wrote:
> Below, I want write_seq to use the accession,
> rather than the default.
> ---------------------------------------------
> #!/usr/bin/perl
>  use Bio::SeqIO;
> 
>   my $infile=shift;
>   $in  = Bio::SeqIO->new(-file => $infile,
>                          -format => 'GenBank');
>   my $outfile= ">" . $infile . ".fa";
>   $out = Bio::SeqIO->new(-file => $outfile,
>                          -format => 'fasta'
>                         );
> 
>   while ( $seq = $in->next_seq() ) {
>    print $seq->accession,"\n";
>    $out->write_seq($seq);
>   }
> ------------------------------------------------
> So, Going to the Bio::Seq docs, I see:
> ---------------------------------------------------------
> preferred_id_type	code	top	prev	next
> 
>  Title   : preferred_id_type
>  Usage   : $obj->preferred_id_type('accession')
>  Function: Get/Set the preferred type of identifier to use in the ">ID"
> position
>            for FASTA output.
>  Returns : string, one of values defined in
> @Bio::SeqIO::fasta::SEQ_ID_TYPES.
>            Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
>  Args    : string when setting. This must be one of values defined in 
>            @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
>            accession, accession.version, display, primary
>  Throws  : fatal exception if the supplied id type is not in
> @SEQ_ID_TYPES.
> ----------------------------------------------------------
> but I have so far been unable to figure out how in fact to
> set the SEQ_ID_TYPE .
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 


-- 
------------------------------------------------------------------
Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Tatzberg 47
01307 Dresden
Germany
Tel. +49-351-4173 137
Fax  +49-351-4173 109

public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg
------------------------------------------------------------------