[Bioperl-l] Convert fastq to fasta

[perlbio007]

Iam new to Bioperl. Pls help.
I have a zip folder of sequences which is in fastq format. I need to convert
it in fasta format?
How I do that using bioperl?What module do I need?

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[Cook, Malcolm]

I don't think you want bioperl for this

try fastq_to_fasta part of http://hannonlab.cshl.edu/fastx_toolkit/

usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]

Malcolm Cook
Stowers Institute for Medical Research - Bioinformatics
Kansas City, Missouri USA

[Tao Zhu]

Scripts like this are ok:

------------- transform.pl ---------------
use Bio::SeqIO;
my ($file1,$file2)=@ARGV;
my $seqin = Bio::SeqIO -> new (-format => 'fastq',-file => $file1);
my $seqout = Bio::SeqIO -> new (-format => 'fasta',-file => ">$file2");

while (my $seq_obj = $seqin -> next_seq)
{
$seqout -> write_seq($seq_obj);
}
-------------------------------------------
run as this:
perl transfrom.pl sequence.fastq sequence.fasta

> Message: 7
> Date: Wed, 27 Apr 2011 17:26:49 -0700 (PDT)
> From: perlbio007 <perlb...@gmail.com>

> Subject: [Bioperl-l] Convert fastq to fasta

> To: Biop...@lists.open-bio.org
> Message-ID: <314925...@talk.nabble.com>
> Content-Type: text/plain; charset=us-ascii

>
>
> Iam new to Bioperl. Pls help.
> I have a zip folder of sequences which is in fastq format. I need to
> convert
> it in fasta format?
> How I do that using bioperl?What module do I need?
>

--
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tz...@mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)

[Florent Angly]

You need to use this module: Bio::SeqIO::fastq
Read this for explanations:
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqIO/fastq.html
Regards,
Florent

On 28/04/11 10:26, perlbio007 wrote:
> Iam new to Bioperl. Pls help.
> I have a zip folder of sequences which is in fastq format. I need to convert
> it in fasta format?
> How I do that using bioperl?What module do I need?

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