[Biopython] internal function to convert illumina quality scores to phred

[Peter]

On Mon, Jan 31, 2011 at 6:50 PM, Alan Bergland <bergland at stanford.edu> wrote:
> Hi all,
>
>        I am trying to convert some code I've written to use
> FastqGeneralIterator rather than SeqIO.parse.  For the most part, it works
> great and there is a big speed improvement.  However, I need to be able to
> convert the quality scores of 6 characters from the Illumina format to
> phred.  I can't seem to find the function to do this.  I'm sure it must
> exist, and I apologize if documentation for it is sitting right there in the
> tutorial - I can't seem to find it.  Can someone point me in the right
> direction?
>
> Cheers,
> Alan

Hi Alan,

Probably something in Bio.SeqIO.QualityIO will do what you want,
consult the module's built in documentation via help(...) in Python
or the online version which is here:
http://www.biopython.org/DIST/docs/api/Bio.SeqIO.QualityIO-module.html

I could be more precise if you could clarify what exactly it is you
want to do with a couple of examples (input, desired output).

If you just want fast Solexa/Illumina FASTQ to Sanger FASTQ or a
PHRED style QUAL file from within Python use Bio.SeqIO.convert
for this.

Peter