[Bioperl-l] dpAlign - pairwise sequence alignment - en masse

Mark A. Jensen maj at fortinbras.us
Thu Feb 5 14:14:17 EST 2009


Manni122-

You run out of sequences in $seqB on the first time through. I would do-

 my @seqB;
 while ( push @seqB, $seqB->next_seq ) { 1; } # or something
 while ( my $seq1 = $seqA->next_seq ) {
     foreach $seq2 (@seqB) {
     ....
    }
 }

I'd probably drop the
 next;
statement, too.

cheers MAJ

----- Original Message ----- 
From: "manni122" <manni122 at hotmail.com>
To: <Bioperl-l at lists.open-bio.org>
Sent: Wednesday, February 04, 2009 9:47 AM
Subject: [Bioperl-l] dpAlign - pairwise sequence alignment - en masse


>
> Hope I am right here.
> I need help in coding the right routine. I have two files with a lot of
> sequences in. I want to pairwise align any Sequence in file A with any
> sequence in file B. My first loop is not working even the next command is
> given. This loop reads just the first sequence in file A and aligns with all
> sequences in file B which means the second loop is working. I appreciate any
> help out of this...
>
> At the moment I have:
>
>  use Bio::Tools::dpAlign;
>  use Bio::SeqIO;
>  use Bio::SimpleAlign;
>  use Bio::AlignIO;
>  use Bio::PrimarySeqI;
>
>  $factory = new Bio::Tools::dpAlign(-match => 3,
>                     -mismatch => -1,
>                     -gap => 3,
>                     -ext => 1,
>                     -alg =>
> Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
>
>
>  $seqA = Bio::SeqIO->new(-file => "A.fas", -format => "fasta");
>  $seqB = Bio::SeqIO->new(-file => "B.fas", -format => "fasta");
>  my $alnout = Bio::AlignIO->new(-format => "clustalw",
>
>                                 -file => ">out.fas");
>
> #reads the first file in and should go through all sequences
>     while( my $seq1 = $seqA->next_seq ) {
>
> #reads the second file in and goes through all sequences
>        while (my $seq2 = $seqB->next_seq) {
>
> $factory = Bio::Tools::dpAlign->new(-alg => 1);
>
>       $out = $factory->pairwise_alignment($seq1,$seq2);
>
>       $alnout->write_aln($out);
>
>            }
> next;
>         }
>
> -- 
> View this message in context: 
> http://www.nabble.com/dpAlign---pairwise-sequence-alignment---en-masse-tp21831861p21831861.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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