[Biopython-dev] [Bug 2403] prosite parser can't handle new PROSITE/PRORULE format

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2403


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

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2007-11-19 06:40 EST -------
Fixed in CVS, and I've also updated the unit test.  Having the test data file
and example script all ready made this much easier, thanks.

As per my email, the order in _scan_fns does matter.  The 'redundancy' you
spotted was commented as an ugly hack.

P.S. I would have used the following style in your script:

handle = open(PROSITEDAT)
iterator = Iterator(handle,RecordParser())
for record in iterator :
    print record.name
    prosite_data.append(record)
handle.close()

rather than:

handle = open(PROSITEDAT)
iterator = Iterator(handle,RecordParser())
record = iterator.next()
prosite_data = []
while record:
    print record.name
    prosite_data.append(record)
    record = iterator.next()
handle.close()


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