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

Hilmar Lapp 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  
Bio::Seq::Quality objects.

	-hilmar

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