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

[Sebastian Bassi]

On Wed, Mar 25, 2009 at 7:01 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Sebastian - could you have a quick play with this github code (using the new
> UnknownSeq class), and the current CVS code (using None), and make sure
> both support the slicing operations you were trying earlier?  Thanks.

First I tried the CVS code (with None in seq), it worked.
Then I tried the git code and it also worked. One thing I noticed is
that I got "?" instead of "N" the "sequence" of the UnknownSeq.
>From a practical point of view, both versions are the same, but the
concept of UnknownSeq looks solid than None, because if I don't know
about about biopython internals, I would never try to slice a None
seq. With "None":
len(s) returns:

Traceback (most recent call last):
  File "/home/sbassi/bioinfo/INTA/qualparser.py", line 21, in <module>
    print len(s)
  File "/home/sbassi/test/virtualenv-1.3.2/t6/lib/python2.5/site-packages/biopython-1.49-py2.5-linux-i686.egg/Bio/SeqRecord.py",
line 481, in __len__
    return len(self.seq)
TypeError: object of type 'NoneType' has no len()

So I would never try to do:
new_s = s[10:30]

But with the UnknownSeq object, len(s) returns an actual length, so it
is more intuitive that it can be sliced.

I liked the github interface, may I setup my own repository?

Best,

-- 
Sebastián Bassi. Diplomado en Ciencia y Tecnología.

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