[Bioperl-l] How to read seq and quals into Bio::Seq::Quality object?

Phillip San Miguel pmiguel at purdue.edu
Mon Jun 30 15:13:47 EDT 2008


    Anyone? Sorry if I'm being a jerk. But on the basis of the existence 
of Bio::Seq::Quality it seems Bio::Seq::SeqWithQuality was deprecated. 
But the latter has a clear methodology to get from .fasta and 
.fasta.qual files into a new object. Once the new object is populated, 
looks like the former might be superior to use.
    But at the moment the only way I'm seeing to populate the ::Quality 
object from two files is to bring each file in with SeqIO and then use 
the primary seq and primary qual objects.  Thus created I'd export their 
sequence and quals as text and use that create the ::Quality object. If 
that is the way to go, fine. But I feel like I must be missing something.

Phillip
Purdue Genomics Core Facility

Phillip SanMiguel wrote:
> What would be the accepted method to read the seq and qual values in 
> from two files (a fasta and a qual file) and put them into 
> Bio::Seq::Quality object. Is there a Bio::SeqIO method that would do 
> that?
>
> Phillip
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