Parsing BLAST results into per-query files

(see thread)

• Remember that Bio::SearchIO can write as well as read. --Ed.

Tim Kohler asks:

When I use Bio::Tools::Run::StandAloneBlast to BLAST one fasta file including different sequences, I get a BLAST output with many queries, each having several hits / sbjcts. My problem is how to parse all hits of one query into a single new file. And this for all the queries I have in my BLAST output file.

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If you have your multiple-query blast report file, you can sort and output separate files like so:

use Bio::Search::Result::BlastResult;
use Bio::SearchIO;
 
my $report = Bio::SearchIO->new( -file=>'full-report.bls', -format => blast);
my $result = $report->next_result;
my %hits_by_query;
while (my $hit = $result->next_hit) {
  push @{$hits_by_query{$hit->name}}, $hit;
}
 
foreach my $qid ( keys %hits_by_query ) {
  my $result = Bio::Search::Result::BlastResult->new();
  $result->add_hit($_) for ( @{$hits_by_query{$qid}} );
  my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format=>'blast' );
  $blio->write_result($result);
}

--Ed.

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Russell also had a solution, but we'll let him pare it down for the scrapbook!