[Bioperl-l] Hit orientation using SearchIO

[Jason Stajich]

TMTOWTDI

You can get the query and hit information as Bio::SeqFeatureI objects  
with
$hsp->query  or $hsp->hit
  SO
$hsp->query->strand
$hsp->hit->strand

This should be demonstrated in the SearchIO HOWTO as well.
-jason
On Dec 18, 2008, at 10:09 AM, Kevin Brown wrote:

> Check the Strand property to determine which orientation the match  
> has.
>
> $hsp->strand('hit')
> $hsp->strand('query')
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Sean ohEigeartaigh
>> Sent: Thursday, December 18, 2008 6:00 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Hit orientation using SearchIO
>>
>> Hi,
>>
>> I'm trying to find out the orientation of blast hits
>> (relative to the query sequence) using SearchIO to process a
>> StandAloneBlast report. I can get the start and end points of
>> the query and the hits using $hsp->start/end('hit'),
>> $hsp->start/end('query') but it always lists the coordinates
>> from lowest to highest. How do I find out if, for example,
>> the query runs 1-60 and the hit runs 240-180? The information
>> is in the BLAST OUT file so it must be accessible.
>>
>> Thanks very much for your time,
>> Seán Ó hÉigeartaigh, bioinformatics phD student.
>>
>>
>>
>>
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>>
>
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Jason Stajich
jason at bioperl.org