[BioPython] Ace parser

[Leighton Pritchard]

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Hi Frank,

One of my .ace output files had a contig whose record ended immediately
after a 'QA' line.  I fixed the problem locally in Ace.py at line 350
with the following after the parser checks for 'QA'.

########

~            read_and_call(uhandle,consumer.qa,start='QA ')
~            # Changed by LP 7/5/04
~            try:
~                read_and_call_while(uhandle,consumer.noevent,blank=1)
~            except SyntaxError:
~                consumer.end_contig
~                return
~            line = safe_peekline(uhandle)
~            if line.startswith('DS'):
~                read_and_call(uhandle,consumer.ds,start='DS ')

########

Again, you might be wanting a more elegant solution ;)

The above also accounts for situations in which my last suggestion (for
the absence of a 'DS' line broke.

Best,

- --
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/lp/index.shtml
T: +44 (0)1382 532761 ext.2405		F: +44 (0)1382 568578
PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net
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