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

[Hilmar Lapp]

He wants the description on the description line, like for the  
sequence file.

Thomas, my guess is the code doesn't print the description to the  
line although I haven't made sure. Do you want to volunteer and  
check, add that print statement and post the patch?

	-hilmar

On May 5, 2006, at 10:04 AM, Brian Osborne wrote:

> 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
>>
>> --------------------------------------------------------------------- 
>> ---------
>> --------------------
>>
>>
>>
>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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