[Bioperl-l] seqIO.pm

[Smithies, Russell]

Or you could use the builtin script bp_sreformat.pl

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Rondon Neto
> Sent: Tuesday, 22 November 2011 6:31 a.m.
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] seqIO.pm
> 
> 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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