[Bioperl-l] <No subject>

[Jason Stajich]

Anthony-

Bonnie's response is dead on use $hsp->hit->start().

There is a rather long-winded reason why this doesn't work with the
current release, however I am happy to say that I've checked in changes
s.t. this will work in the next stable release.

-jason

On Mon, 8 Jul 2002 AUnderwood@PHLS.org.uk wrote:

> Hi all,
>
> I am having a problem when parsing blast output from Standalone Blast. I am specifying "Blast" as the READMETHOD in the parameters passed to the
> Standalone package.
> However when I try to find the start of the hit using the following line:
>
> print OUT "start of hsp: ", $hsp->start('sbjct') ,"\n";
>
> the output is   start of hsp: sbjct not                 start of hsp: 12345    where 12345 is the starting point
> if the blast hit within the subject.
>
> If instead the line is
> print OUT "start of hsp: ", $hsp->start() ,"\n";
>
> then I do  get a value which is probably the default, equivalent to
> $hsp->start('query')
>
> Please can anyone tell me how I can get the value for the start of the blast
> hit in the subject.
>
> Many thanks,
>
>
> Anthony
>
>
>
> Dr Anthony Underwood
> Bioinformatics Unit
> Central Public Health Laboratory
> 61 Colindale Avenue
> London
> NW9 5HT
> t:    0208 2004400 ext. 3618
> f:    0208 3583138
> e: aunderwood@phls.org.uk
>
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu