[Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1747

biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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 Attachment #198 is|0                           |1
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------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2005-03-09 11:34 -------
Created an attachment (id=200)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=200&action=view)
Patch to the class _Scanner in Bio/GenBank/__init__.py

This version of the patch completely replaces the Martel code in the class
_Scanner.

The feature parsing code has (in my opinion) been simplified (since the
previous patch).

However, with all the new code added to deal with the "GenBank header section",
the feed function is probably ripe for splitting up into sub functions.

This has been fully tested with the Tests/test_GenBank.py as shipped with
Biopython 1.40b.

As before, patch created on Windows XP with the Cygwin diff command against
Bio/GenBank/__init__.py revision 1.53 (shipped with BioPython 1.30 and 1.40b):

diff my_version.py vcs_version.py > patch.txt



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