[Biopython-dev] [Bug 2848] SeqIO fastq routines reject valid quality socres

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2848





------- Comment #7 from pmmagic at gmail.com  2009-06-05 09:36 EST -------
(In reply to comment #6)
> (In reply to comment #5)
> > HI Peter,
> > 
> > The problem arises in parsing the fastq formatted consensus mappings
> > produced by MAQ, so these are "mapping qualities" rather than read
> > qualities directly.
> 
> I see - that does explain why there are sometimes very very good quality
> scores. Presumably maq limits itself to a maximum PHRED quality of 93?

I presume so. If not that would contradict their own specification.

> 
> > Here's a simple snippet that is valid fastq:
> > 
> > @ref|NC_001133|
> > nnnnnnnnnnnnnnnacacccacacaccacaccacacaccACACCACACCCACACACACA
> > CATCCTAACACTACCCTAACACAGCCctaatcyaacCCTGACCAACCTGTCTCTCAACTT
> > +
> > !!!!!!!!!!!!!!!@EHHHHHHKKJKKKKNNNBN:NNNNQQQQQABGA?LTTWWWZZZI
> > HEFBZLZ]]]]]]]]]ZZZZZT at TTQQQT4A]1?cfiloxL{xuuux{]~~~~~Ake~`~
> 
> May we use that for a unit test in Biopython?

Absolutely.

Cheers,
Paul


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