[Bioperl-l] SeqIO problem

Schreiber, Mark mark.schreiber@agresearch.co.nz
Mon, 26 Feb 2001 13:06:43 +1300

Hi I seem to have a problem on my system reading fasta libraries.

Initially I thought it was the format of my fasta file however the
seq1.fasta file from the examples directory of the bioperl distribution
gives the same problem. Only one sequence is read from the file!

Here is the script:

#!/usr/bin/perl -w

use strict;
use Bio::Seq;
use Bio::SeqIO;

my $input = shift;

my $seqin  = Bio::SeqIO->new('-format' => 'Fasta',
                             -file => "$input"

my @seqs = ();
while(my $sequence = $seqin->next_primary_seq() ){
    push @seqs, $sequence  

print "No Seqs:\t" . length(@seqs). "\n";

exit 0;


The number of seqs output is always 1.

I am using bioperl 0.6.2 on a DEC Alpha with true64. Perl version 5.004_04
built for alpha-dec_osf

Can anyone help?