[Bioperl-l] [Bioperl]problem with E-value
cjfields at uiuc.edu
Wed Jan 17 17:03:56 UTC 2007
On Jan 17, 2007, at 10:54 AM, Sendu Bala wrote:
> Chris Fields wrote:
>> I pretty sure I know exactly what the problem is and how to fix it
>> (if you haven't done it already). Looks like the parser trashes
>> the rest of the BLAST results data since it's not catching the
>> next BLAST report header (and not breaking out of the while()
>> loop). That may be what is triggering the e-value error. I have
>> been parsing new BLAST reports recently w/o that one popping up,
>> but it may be a difference between the web BLAST report and the
>> executable (wouldn't be the first time that has happened.
>> Did you want me to take a look?
> Sure. In case you didn't notice, the reason it isn't catching the
> next BLAST report is the lack of alignments. For the few results
> that do have alignments, that's where it 'works'.
I plan on generating a new BLAST report (from the web, since I don't
have 2.2.15 installed) with multiple queries and no alignments to see
what happens (i.e. see if the new multiquery report is similar to
this one). If so, there is a 'wrap-up' section of the parser, where
hit data not in alignments (in the table only) is used to generate
Hit objects; it's dropping this data likely b/c there is no regex
signalling the next result event.
More information about the Bioperl-l