[Bioperl-l] A problem parsing BLASTX 2.2.8 reports

[Matthew Links]

I have run into a problem parsing BLASTX reports (version 2.2.8). When I
ask for strand and frame on the Bio::Search::Hit::HitI object I am
getting back the wrong answer. 

I think this has to do with a slight formatting change in the BLAST
output.

--- BLASTX 2.2.5 ---

>gi|19879878|gb|AAM00191.1| guanine nucleotide-exchange protein GEP2
            [Oryza sativa]
          Length = 1789
 
 Score =  320 bits (819), Expect(2) = 7e-98
 Identities = 160/193 (82%), Positives = 173/193 (89%)
 Frame = +2

--- BLASTX 2.2.8 ---

>gi|38346787|emb|CAE02205.2| OSJNBa0095H06.12 [Oryza sativa (japonica
            cultivar-group)]
          Length = 1724
 
 Score =  102 bits (254), Expect = 5e-21
 Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 30/204
(14%)
 Frame = +2

In my debugging it looks like everything is ok except for the
strand/frame data. Which when parsing 2.2.8 gets

hit->frame = 1
hit->strand('query') = 1
hit->strand('hit') = 0

Has anyone seen this problem before? 

Thanks in advance,

Matt

-- 
Matthew Links

Research Officer, Bioinformatics
Department of Computer Science
University of Saskatchewan
1C101 Engineering Building
57 Campus Drive
Saskatoon Saskatchewan
S7N 5A9
Canada

Tel:	(306) 966 2058
Fax:	(306) 966 2033
Email:	mlinks at cs.usask.ca