[Biopython-dev] [Bug 2848] SeqIO fastq routines reject valid quality socres
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Thu Jun 4 20:54:59 UTC 2009
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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