[Bioperl-l] Bio::Seq::Quality description line problem

[Brian Osborne]

T.D.,

According to the documentation,
http://www.bioperl.org/wiki/Qual_sequence_format, your *qual file looks
right. What are you trying to create?

Brian O.


On 5/4/06 12:50 PM, "T.D. Houfek" <thoufek at pngg.org> wrote:

> Using Bioperl 1.5, having trouble with writing FASTA-style quality files
> using Bio::Seq::Quality.
> 
> I create the Bio::Seq::Quality object, giving its constructor an ID, a
> description, a nucleotide sequence, and a quality sequence. I then write
> the sequence FASTA and the quality FASTA. The description string will
> appear in the header line of the sequence FASTA, but not in the header
> line of the quality FASTA.
> 
> Can anybody help me figure out how to fix this? I've attached a sample
> script and output.
> 
> -T.D.
> 
> ------------------- sample script follows
> ---------------------------------------
> 
> #!/usr/bin/perl
> use strict;
> use Bio::Seq::Quality;
> use Bio::SeqIO;
> 
> my $id = "bogus_id";
> my $desc = "bogus description";
> my $seq = "ATTATTATTATTATT";
> my $qual = "10 20 30 10 20 30 10 20 30 10 20 30 10 20 30";
> 
> my $sequal_obj = Bio::Seq::Quality->new(
> -display_id => $id,
> -desc => $desc,
> -seq => $seq,
> -qual => $qual
> );
> 
> my $qualout = Bio::SeqIO->new(
> -file => ">myfile.qual",
> -format => 'qual'
> );
> my $seqout = Bio::SeqIO->new(
> -file => ">myfile.seq",
> -format => 'Fasta'
> );
> 
> $seqout->write_seq($sequal_obj);
> $qualout->write_seq($sequal_obj);
> 
> 
> ------------------ sample output follows
> ---------------------------------------
> 
> tdhoufek at aether:~$ cat myfile.seq
>> bogus_id bogus description
> ATTATTATTATTATT
> tdhoufek at aether:~$ cat myfile.qual
>> bogus_id
> 10 20 30 10 20 30 10 20 30 10 20 30 10 20 30
> 
> ------------------------------------------------------------------------------
> --------------------
> 
> 
>