[Bioperl-l] BPlite to parse multi query sequence report

[nkuipers]

This should do the trick.

#parse the BLAST report
	my $parser = Bio::Tools::BPlite->new( -file => $toBeParsed );
	{
	while ( my $subject = $parser->nextSbjct ) {
		while ( my $hsp = $subject->nextHSP ) { #your code here
		}
	}
	last if $parser->_parseHeader == -1;
	redo;
	}

>===== Original Message From "E Klee" <klee_17@hotmail.com> =====
>Ok, I am still struggling w/ the BioPerl Blast parsers.  Can I use BPlite to
>parse a blast output file that contains multiple query sequences compared to
>multiple subject sequences.  My experience with this so far is openning a
>new BPlite report will only reference the output for the first query
>sequence in my file.  Using a while() statement to step through all subjects
>via nextSbjct() is only finding the hits to the first query sequence.  Any
>help?
>
>-E
>
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