[Biopython-dev] [Bug 1972] New Prosite comment qualifier breaks Bio.Prosite.RecordParser

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1972





------- Comment #1 from bill at barnard-engineering.com  2006-03-21 02:28 -------
Created an attachment (id=298)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=298&action=view)
Proposed patch to update the parser

The fix is quite simple; add a clause to Bio.Prosite. _RecordConsumer.comment()
to assign the new version qualifier to a new Bio.Prosite.Record data member
named following the existing naming convention.

Most of the patch consists of updates to the data files in the Tests directory
that are tested by Tests/test_prosite2.py

I would further recommend removing the following files from the repository
since they are not used in (or refer to) any existing test that I found. These
are all in the Tests/Prosite directory:

README
ps001
ps002
ps003
ps00107.htm
ps00123.htm
ps00123.txt
ps00159.htm
ps00165.htm
ps00213.html
ps00213.txt
ps00432.htm
ps00812.txt
ps01213.txt

The test_prosite2 tests pass before and after applying the patch to the current
CVS tree.

Patch application instructions:

Run from the top of the tree, i.e. in the biopython root directory
% patch -p0 < path_to_patches/biopython-Bio_Prosite_parser_fix.patch




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