[Bioperl-l] Bio::SearchIO

[Jason Stajich]

It should still work.

You may try:
$hsp->query->start
$hsp->query->end

$hsp->hit->start
$hsp->hit->end

This should be equivalent with
$hsp->start('hit'), $hsp->end('hit'), ... etc

But it is possible that something has been changed in the object layer
that broke this.  I'm not really sure since it should be in the tests...

if you can post code + an example BLAST file as a bug report at
http://bugzilla.bioperl.org which demonstrates the problem we'll have a
look.

-jason

On Tue, 27 Jul 2004, davila wrote:

> I was using the last year a Blast parser with the following lines:
>
>        $query_start=$hsp->start('query');
>        $query_end=$hsp->end('query');
>        $hit_start=$hsp->start('hit');
>        $hit_end=$hsp->end('hit');
>
> however it is no longer working and I had to comment them in order to have the parser working. If there were any changes, how I could now catch the "query_start", "query_end", "hit_start" and "hit_end" from the Blast results ?
>
> Thanks in advance, Alberto
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu