[Bioperl-l] Creating a fastq format file?
Mark A. Jensen
maj at fortinbras.us
Wed Apr 22 09:33:08 EDT 2009
Dan- There is a fastq module under Bio::SeqIO. Do something like
# from Bio::Seq::Quality synopsis...
my $qual = '0 1 2 3 4 5 6 7 8 9 11 12';
my $trace = '0 5 10 15 20 25 30 35 40 45 50 55';
my $seq = Bio::Seq::Quality->new
( -qual => $qual,
-trace_indices => $trace,
-seq => 'atcgatcgatcg',
-id => 'human_id',
-accession_number => 'S000012',
-verbose => -1 # to silence deprecated methods
# typical Bio::SeqIO call
$seqio = Bio::SeqIO( -file => ">your_file", -format=>'fastq');
----- Original Message -----
From: "Dan Bolser" <dan.bolser at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, April 22, 2009 6:49 AM
Subject: [Bioperl-l] Creating a fastq format file?
> Creating a fastq format file from fasta and 'fasta quality file'?
> I'm sure this is easy, but I'm still not able to 'think bioperl'...
> I have a 'fasta quality file' and a fasta file, and I would like to
> output a fastq file. I followed the discussion on the previous thread
> With the conclusion seeming to be 'just do it'. Could someone point me
> at a way to do this, or was that suggestion an error? i.e. the poster
> was working out a way to create a fastq the only way possible...
> I get the feeling that this should be a one-liner, but perhaps the
> above thread was demonstrating the code I need to copy.
> Thanks for any suggestions,
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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