[BioPython] Prosite / Prorule
holger.dinkel at gmail.com
holger.dinkel at gmail.com
Fri Nov 16 05:38:56 EST 2007
Hello List,
I just stumbled upon an error with the parsing of a 'newer' (>20) version of
Prosite: Prosite introduced a new field called ProRules which cause errors
in parsing with Bio/Prosite/__init__.py / Bio/ParserSupport.py.
I updated biopython to 1.44, but the error persists.
Here is the Traceback:
----------------------------------------------------------------------------------------------------
File "/usr/lib/python2.4/site-packages/Bio/Prosite/__init__.py", line 227, in next
return self._parser.parse(File.StringHandle(data))
File "/usr/lib/python2.4/site-packages/Bio/Prosite/__init__.py", line 349, in parse
self._scanner.feed(handle, self._consumer)
File "/usr/lib/python2.4/site-packages/Bio/Prosite/__init__.py", line 381, in feed
self._scan_record(uhandle, consumer)
File "/usr/lib/python2.4/site-packages/Bio/Prosite/__init__.py", line 396, in _scan_record
fn(self, uhandle, consumer)
File "/usr/lib/python2.4/site-packages/Bio/Prosite/__init__.py", line 477, in _scan_do
self._scan_line('DO', uhandle, consumer.documentation, exactly_one=1)
File "/usr/lib/python2.4/site-packages/Bio/Prosite/__init__.py", line 418, in _scan_line
read_and_call(uhandle, event_fn, start=line_type)
File "/usr/lib/python2.4/site-packages/Bio/ParserSupport.py", line 300, in read_and_call
raise SyntaxError, errmsg
SyntaxError: Line does not start with 'DO':
PR PRU00498;
----------------------------------------------------------------------------------------------------
I tried to figure out, where the problem lies, but I do not really understand
the structure of the parsing modules in 'Bio/Prosite/__init__.py'
I tried to create a new entry for the prorule:
define a
def _scan_pr(self, uhandle, consumer):
self._scan_line('PR', uhandle, consumer.identification, up_to_one=1)
add that to the '_scan_fns' and so on, but then the scanning order seems to get
out of order, and i get a different "SyntaxError: Line does not start with ..."
error...
Is the parsing mechanism described anywhere, so I can look it up and fix the error?
Regards,
Holger
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