Michiel de Hoon
mdehoon at c2b2.columbia.edu
Sun Feb 25 11:42:21 UTC 2007
> The file format is now a required argument (it can be made into an
> optional argument in future if we decide to support file format guessing
> one day).
Looks good! I have just some minor comments:
Currently the format has to be in lower-case. It might be better to make
the format case-insensitive. So I won't have to remember whether it is
"fasta", "Fasta", or "FASTA".
Three of the ValueErrors raised by WriteSequences and SequenceIterator
are actually TypeErrors:
if isinstance(handle, basestring) :
if not format :
if not isinstance(format, basestring) :
The "if not format" is actually not needed, since Python will complain
already if these functions are called without the correct number of
For an incorrect format argument, WriteSequences raises an
AssertionError. A ValueError (as in SequenceIterator) seems more
appropriate. Also, it might be a good idea to print possible values for
the format if the user passes an incorrect format.
Btw, the docstring for SequenceIterator mentions guessing the file
format from the handle if the format is not specified.
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