You'll get better help on the Bioperl mailing list and website.

Bio::SeqIO next_seq returns Bio::Seq objects. Follow the SYNOPSIS and you can't go wrong. 

my $seqio = Bio::SeqIO->new(-format => $seqformat, -file =>$filename);
while( my $seq = $seqio->next_seq ) {
 print "seq name is ", $seq->display_id, 
       " desc is ", $seq->description(), "\n";
 print "sequence is ", $seq->seq(), "\n";
}

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You can do magic stuff if you want to treat it like a filehandle too (although I doubt this is what you were trying to do) 
my $fh = Bio::SeqIO->newFh(-format =>$seqformat, -file =>$filename);
while(<$fh>) {
 my $seq = $_;
 # do as before
}

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You can also process filehandles (all XXIO modules in Bioperl support this if the inherit from Bio::Root::IO). Usefile if you are pipine output from a program with your script and want to capture the stream and make it Bio::Seq objects. 
my $fh;
open($fh, "cat seqfile |") ||die $!;
my $seqio = Bio::SeqIO->new(-format => $seqformat, -fh => $fh);

# OR retrieve a sequence from the blast formatted db 'nt'
#    by GI number 

open(IN, "fastacmd -d nt -s 3264957 |") ||die $!;
my $seqio = Bio::SeqIO->new(-format => 'fasta',-fh => \*IN);
while( my $seq = $seqio->next_seq ) {
 #and so forth....
}

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In reply to Re: Not sure about Bio::SeqIO by stajich
in thread Not sure about Bio::SeqIO by MonkPaul

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