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

[Hilmar Lapp]

This is a property of the SeqIO stream, so you need to set it on the 
stream object:

	$seqio = Bio:SeqIO->new(-format=>'fasta',-file=>"<blah.fa");
	$seqio->preferred_id_type('accession');

Hth,

	-hilmar
	
On Tuesday, April 5, 2005, at 10:08  AM, Cook, Malcolm wrote:

> hmmm - this is new to me
>
> let's see, on my bioperl 1.5 installation, the unix one-liner
>
>  perl -MBio::SeqIO::fasta -e 'print "@Bio::SeqIO::fasta::SEQ_ID_TYPES"'
>
> returns
>
> accession accession.version display primary
>
> so, I think you should be able to add, for instance
>
> $seq->preferred_id_type('display')
>
> or, in your case
>
> $seq->preferred_id_type('accession')
>
> just before your call to write_seq
>
> try it!
>
> Malcolm Cook - mec at stowers-institute.org - 816-926-4449
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, MO  USA
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Jonathan
> Miller
> Sent: Monday, April 04, 2005 6:45 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] newbie needs help with "preferred_id_type"
>
>
>
> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------