[BioPython] Different parse error in ace.py

[Leighton Pritchard]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi all,

The Ace.py parser assumes that the DS tag will always be present in
Phrap output.  Unfortunately, it isn't always present in my output, and
so the parser gave me this traceback:

uncaught: (<class exceptions.SyntaxError at 0xbf51b74c>,
<exceptions.SyntaxError instance at 0xbf03f4cc>)
Traceback (most recent call last):
~  File
"/usr/local/lib/python2.3/site-packages/ScriptFramework/script.py", line
241, in main
~    self.run()
~  File "/home/lpritc/Data/scripts/draw_ace.py", line 71, in run
~    self.ace_file_record = self.load_record()       # Load ACE file
~  File "/home/lpritc/Data/scripts/draw_ace.py", line 97, in load_record
~    ace_file_record = parser.parse(self.input)
~  File "/usr/local/lib/python2.3/site-packages/Bio/Sequencing/Ace.py",
line 295, in parse
~    rec=iter.next()
~  File "/usr/local/lib/python2.3/site-packages/Bio/Sequencing/Ace.py",
line 218, in next
~    return self._parser.parse(File.StringHandle(data))
~  File "/usr/local/lib/python2.3/site-packages/Bio/Sequencing/Ace.py",
line 234, in parse
~    self._scanner.feed(uhandle, self._consumer)
~  File "/usr/local/lib/python2.3/site-packages/Bio/Sequencing/Ace.py",
line 331, in feed
~    self._scan_record(handle, consumer)
~  File "/usr/local/lib/python2.3/site-packages/Bio/Sequencing/Ace.py",
line 352, in _scan_record
~    read_and_call(uhandle,consumer.ds,start='DS ')
~  File "/usr/local/lib/python2.3/site-packages/Bio/ParserSupport.py",
line 300, in read_and_call
~    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'DS ':
RT{

I've fixed it locally by changing line 352 in Ace.py to

###

if attempt_read_and_call(uhandle,consumer.ds,start='DS '):
~                read_and_call(uhandle,consumer.ds,start='DS ')

###

so as to take the possible absence of a DS tag into account, though you
may want to do something more elegant with the real code ;)

- --
Dr Leighton Pritchard AMRSC
D104, PPI, Scottish Crop Research Institute
Invergowrie, Dundee, DD2 5DA, Scotland, UK
E: lpritc at scri.sari.ac.uk	W: http://bioinf.scri.sari.ac.uk/index.shtml
T: +44 (0)1382 568579		F: +44 (0)1382 568578
PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.2.3 (GNU/Linux)
Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org

iD8DBQFAg8dvL1gZ+OWLpBsRAllhAJ4kgHrygUcTVozoyKH2XlLTBE+07ACfRWZ1
5T0Ztu63f1flGaxHJSs0QZA=
=zTh4
-----END PGP SIGNATURE-----