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

Jason Stajich jason.stajich at duke.edu
Tue Feb 28 12:36:34 EST 2006


On Feb 28, 2006, at 5:01 AM, Edward WIJAYA wrote:

> Hi,
>
> Does Bio::SeqIO has a method  specially designed for
> reading all the sequences from a fasta file into array.
>
no but feel free to contribute one.
> What I have currently is this subroutine, it seems to me
> __very inefficient__. I was wondering
> is there a better way to achieve it.
>
Do you have a reason to think this is the slow part of your algorithm  
or are you just going on a gut reaction?  There is certainly overhead  
in calling a method but I am pretty sure that it isn't that  
significant, depends on how many sequences you are reading in I guess.

Just write a next_seq_array method and have it put the seqs onto an  
array within the method and do a benchmark test to show that it is  
faster.

-jason
>
> 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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> Bioperl-l at lists.open-bio.org
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




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