[Bioperl-l] Bio::SeqIO -- Reading Formated sequence file (Fasta) into Array

Edward WIJAYA ewijaya at singnet.com.sg
Tue Feb 28 05:01:23 EST 2006


Hi,

Does Bio::SeqIO has a method  specially designed for
reading all the sequences from a fasta file into array.

What I have currently is this subroutine, it seems to me
__very inefficient__. I was wondering
is there a better way to achieve it.


sub get_sequence_from_fasta {
     my $file = shift;
     my @seqs= ();

     open INFILE, "<$file" or die "$0:  Can't open file $file: $!";
     my $in = Bio::SeqIO->new(-format => 'fasta',
                              -noclose => 1 ,
                              -fh => \*INFILE);

     while ( my $seq = $in->next_seq() ) {
        push @seqs, $seq->seq();
     }
     return @seqs;
}


BTW, I also have tried to do this. I thought
this might be a better way to do the above job.
but it doesn't work.

sub get_sequence_from_fasta_that_doesnot_work {
     my $file = shift;
      open my fh, "<$file" or die "$0:  Can't open file $file: $!";
     my $in = Bio::SeqIO->newFh( -format => 'fasta', -fh => $fh );
     return <$in>;
}

Hope to hear from you again.

--
Regards,
Edward WIJAYA
SINGAPORE


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