[Bioperl-l] help using SEARCH IO to parse blast results

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Nov 27 14:31:29 EST 2007


Do the hits need to be sorted first or is this done automagicly?
I ask this as I know Megablast doesn't provide sorted output for most of
it's formats.

Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of Dave Messina
> Sent: Wednesday, 28 November 2007 6:56 a.m.
> To: alison waller
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] help using SEARCH IO to parse blast results
> 
> Hi Alison,
> As Sendu mentioned, the key bit is adding a condition to the hit loop
to
> limit the number of hits that are printed. I didn't test the below
> extensively, but give it a try...
> 
> 
> Dave
> 
> 
> 
> #!/usr/local/bin/perl -w
> 
> # Parsing BLAST reports with BioPerl's Bio::SearchIO module
> # alison waller November 2007
> 
> use strict;
> use warnings;
> use Bio::SearchIO;
> 
> my $usage = "to run type: blast_parse_aw.pl <blast report> <# of
hits>\n";
> if (@ARGV != 2) { die $usage; }
> 
> my $infile  = $ARGV[0];
> my $outfile = $infile . '.parsed';
> my $tophit  = $ARGV[1]; # to specify in the command line how many hits
>                         # to report for each query
> 
> #open(  IN, $infile )     || die "Can't open inputfile $infile! $!\n";
> open( OUT, ">$outfile" ) || die "Can't open outputfile $outfile!
$!\n";
> 
> my $report = new Bio::SearchIO(
>     -file   => "$infile",
>     -format => "blast"
> );
> 
> print OUT
>
"Query\tHitDesc\tHitSignif\tHitBits\tEvalue\t%id\tAlignLen\tNumIdent\tga
ps\t
> Qstrand\tHstrand\n";
> 
> # Go through BLAST reports one by one
> while ( my $result = $report->next_result ) {
>     my $i = 0;
>     while (  ( $i++ < $tophit ) && (my $hit = $result->next_hit) ) {
>         while ( my $hsp = $hit->next_hsp ) {
> 
>             # Print some tab-delimited data about this hit
>             print OUT $result->query_name,     "\t";
>             print OUT $hit->name,              "\t";
>             print OUT $hit->significance,      "\t";
>             print OUT $hit->bits,              "\t";
>             print OUT $hsp->evalue,            "\t";
>             print OUT $hsp->percent_identity,  "\t";
>             print OUT $hsp->length('total'),   "\t";
>             print OUT $hsp->num_identical,     "\t";
>             print OUT $hsp->gaps,              "\t";
>             print OUT $hsp->strand('query'),   "\t";
>             print OUT $hsp->strand('hit'),     "\n";
>         }
>     }
> 
>     if ($i == 0) { print OUT "no hits\n"; }
> }
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