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

[Jason Stajich]

you can - but it is hacky.  The code in SYNOPSIS shows how to do this.

However, I would suggest using Bio::SearchIO instead of BPlite.
See the HOWTO:
http://bioperl.org/HOWTOs/

use Bio::Tools::BPlite;
my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);

  {
    $report->query;
    $report->database;
    while(my $sbjct = $report->nextSbjct) {
        $sbjct->name;
        while (my $hsp = $sbjct->nextHSP) {
            $hsp->score;
            $hsp->bits;
            $hsp->percent;
            $hsp->P;
            $hsp->match;
            $hsp->positive;
            $hsp->length;
            $hsp->querySeq;
            $hsp->sbjctSeq;
            $hsp->homologySeq;
            $hsp->query->start;
            $hsp->query->end;
            $hsp->hit->start;
            $hsp->hit->end;
            $hsp->hit->seq_id;
            $hsp->hit->overlaps($exon);
        }
    }

    # the following line takes you to the next report in the stream/file
    # it will return 0 if that report is empty,
    # but that is valid for an empty blast report.
    # Returns -1 for EOF.

    last if ($report->_parseHeader == -1);
    redo;
  }

On Tue, 14 Jan 2003, E Klee wrote:

>
> 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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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu