[Bioperl-l] How to read seq and quals into Bio::Seq::Quality object?
hlapp at gmx.net
Mon Jun 30 17:25:32 EDT 2008
Apologies if this is a stupid comment, but have you looked at the
Bio::SeqIO::qual format parser? Purportedly, it returns
On Jun 30, 2008, at 3:13 PM, Phillip San Miguel wrote:
> 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 that?
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
More information about the Bioperl-l