[Biopython-dev] Jython 2.7b2 - test_NCBITextParser.py and test_Pathway.py

[Fields, Christopher J]

On May 7, 2014, at 12:21 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, May 7, 2014 at 5:50 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> ...
>> (This looks like a regression in Jython being stricter here, since
>> the error doesn't say which method(s) are too long, fixing this
>> is a bit painful... perhaps counting lines per method would
>> spot the problem methods nicely?)
> 
> Does anyone fancy that fairly boring task? We'd like to get
> rid of the NCBI plain text BLAST parser at some point - but
> anecdotally people continue to use it.

Just as an aside re: the pain of plain-text parsing: if you need an extra data point, this is the same problem we’ve had with bioperl’s (patched-to-death) BLAST parser.  

chris