[Biopython-dev] SeqIO and qual: Question about reading and writing qual files

[Sebastian Bassi]

On Tue, Mar 24, 2009 at 12:13 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
....
> characters using a DNA alphabet. What would you expect to get if you
> used Bio.SeqIO to write out the file in FASTA format?  To my mind there
> are two sensible options - write out the file using the "NNN....N"
> sequence, or raise an error.

"N" is OK (with the same length of the qual file), that is what ABI
does when the QV is low. This is not the same case but I always think
of "N" as "unknown".
Raise an error is not bad because I don't see the need to go from an
non-sequence qual to a fasta (it doesn't make sense). But that I don't
see the need, doesn't means someone else may have a reason.
Best,

-- 
Sebastián Bassi. Diplomado en Ciencia y Tecnología.

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