[Bioperl-l] Re: blast.pl parsing

[Seth Redmond]

I'm trying to parse from an NCBI blast file such that I can get the 
positions of hsp's on the subject strand.

      $blast = Bio::Tools::Blast->new('-file'   => $infile,
	     					'-signif' => 1e-5,
	     						'-parse'  => 1,
							     '-stats'  => 1,
							     '-check_all_hits' => 1, );

	     $num_hits =  $blast->num_hits;
	     for ($j=0; $j<=($num_hits-1); $j++)
	     			{
				     @matches = $hits[$j]->hsp->seq_inds('sbjct', 'id');
         ...etc

Although I can get to each hit (that is, each different matching strand in 
my database) I am having problems where there is more than one match on the 
same sequence, in that the script only parses out the first match.

any advice would be much appreciated.

Seth Redmond



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