[Bioperl-l] Creating a fastq format file?

[Chris Fields]

On Apr 27, 2009, at 10:53 AM, Heikki Lehvaslaiho wrote:

> 2009/4/27 Chris Fields <cjfields at illinois.edu>:
>> This is going within Bio::Seq::Quality, correct?
>
> Yes.
>
> Does Bio::Seq::Quality
>> have a method that indicates what format the quality scores are  
>> actually in
>> (sanger/illumina/illumina1.3/phred/foo)?  The reason I worry about  
>> this is
>> quality scores appear inseparable from their quality format (ranges  
>> vary in
>> length, for instance).
>
> No method.
>
>> For instance, if I picked a Bio::Seq::Quality out of the blue,  
>> could I tell
>> which quality format it originated from w/o guessing, and similarly  
>> could I
>> accurately convert it to another qual format?  To me it seems we need
>> something in Bio::Seq::Quality akin to the alphabet() method used for
>> sequence data.
>
> The text formats encode the quality values in different ways, but they
> are all stored as integer arrays in the object. Converting between
> them is relatively easy.
>
> You are right: quality_format() or even plain format() is needed. The
> SeqIO methods creating the objects should be setting it. Warnings for
> unset format values should be added to appropriate places.
>
>   -Heikki

Agreed, and any conversion methods could default to using a set  
quality_format()/format() for conversions to/from ascii (might serve  
as a good verification point as well).

chris