[Bioperl-l] newbie needs help with "preferred_id_type"
Jonathan Miller
millerj at bcm.tmc.edu
Mon Apr 4 19:44:36 EDT 2005
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 .
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