[Bioperl-l] SearchIO and bl2seq blast reports

[Jason Stajich]

Should work - we have tests in the bioperl-live code for strandedness 
and bl2seq reports for blastn and tblastn.

in t/SearchIO.t
ok($hsp->query->start, 94);
ok($hsp->query->end, 180);
ok($hsp->query->strand, 1);
ok($hsp->hit->strand, -1);
ok($hsp->hit->start, 1);

I don't remember if this bug was fixed before 1.4 went out but 
SearchIO::blast parsing was definitely updated for several bugs since 
1.4.0 release.

Can you post a report and exact code that you are testing as a bug 
report to http://bugzilla.open-bio.org and someone can have a looksie.

-jason
On Nov 29, 2004, at 8:04 PM, Bill Kenworthy wrote:

> Hi, what is the best way to detect strandedness using SearchIO parsing
> bl2seq reports?  Or should I go back to BPLite which I think works.
>
> There were bugs posted about this in the past, but SearchIO in 1.4 is
> still returning 0 for frame and strand on both hit and query with any
> form of bl2seq I have tried.
>
> BillK
>
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/