[Bioperl-l] seqIO.pm

[Rondon Neto]

Hi! try this script:

#!/usr/bin/perl
use warnings;
use strict;
use Bio::SeqIO;

if (!$ARGV[0]) { die "\n### USAGE::: perl $0 [file.fastq]\n"; }

my $fastq = $ARGV[0];

my $in = Bio::SeqIO->new( -file => $fastq,
                          -format => 'fastq' );

my $out = Bio::SeqIO->new ( -file => ">out.phd",
                            -format=> 'phd');

while (my $seq = $in->next_seq()) {
      $out->write_seq($seq);
}

exit;


Best wishes,
Rondon, a brazilian friend.






________________________________
 De: Peter Cock <p.j.a.cock at googlemail.com>
Para: Nathan Taylor <zntayl at gmail.com> 
Cc: bioperl-l at bioperl.org 
Enviadas: Segunda-feira, 21 de Novembro de 2011 14:15
Assunto: Re: [Bioperl-l] seqIO.pm
 
On Thu, Nov 17, 2011 at 1:07 AM, Nathan Taylor <zntayl at gmail.com> wrote:
> Hello,
>
>   Can SeqIO.pm convert a file of fastq reads into .phd files. Or,
> barring that, a file of fastas and file of quals into .phd files?
>
> Many thanks,
> Nathan

In principle that is possible (e.g. Biopython can do fastq to phd).
Have you tried using BioPerl's SeqIO to do this? Was there an
error message?

Peter

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