[Bioperl-l] <No subject>

[BHurwitz@twt.com]

Hi Anthony,

Try the following:

my $start = $hsp->hit->start(); # hit start
my $end = $hsp->hit->end(); # hit end


Regards,
Bonnie



                                                                                                                                                  
                    AUnderwood@PHLS.o                                                                                                             
                    rg.uk                    To:     bioperl-l@bioperl.org                                                                        
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                    bioperl-l-admin@b        Subject:     [Bioperl-l] <No subject>                                                                
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                    07/08/2002 12:39                                                                                                              
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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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