[BioPython] 1.00a2 bug report (+ kludge fix)
Jeffrey Chang
jchang@SMI.Stanford.EDU
Wed, 1 Aug 2001 09:43:00 -0700
Hi Jan,
This is indeed a bug in the current release. Andrew Dalke noted it
earlier and provided the fix:
def read(self, size=-1):
if size == -1:
saved = string.join(self._saved, "")
self._saved[:] = []
else:
saved = ''
while size > 0 and self._saved:
if len(self._saved[0]) <= size:
size = size - len(self._saved[0])
saved = saved + self._saved.pop(0)
else:
saved = saved + self._saved[0][:size]
self._saved[0] = self._saved[0][size:]
size = 0
return saved + self._handle.read(size)
This is in CVS now and will be incorporated into the next release.
>As a remark regarding distinction of error messages versus GenBank records
>in the HTTP response, it might be a better method to look at the MIME type
>of the response. This is text/plain in case of a successful record retrieval,
>but text/html if errors are reported. This might serve as as a basis for
>additional / improved methods for error detection.
Yes, that's a really good idea. It'll take a bit of work to
incorporate within the current framework, but I think it would be
useful. Another thing on the to-do list!
Thanks,
Jeff