[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.
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
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