[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 #6 from biopython-bugzilla at maubp.freeserve.co.uk  2009-06-04 16:54 EST -------
(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?

> 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?

Thanks,

Peter


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