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Blast result parser with Perl and Bioperl

#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU General Public License. # This script will parse a NCBI blastx output file and output the top N hits of each blast search result. # For each hit, the following results are reported: # accesion number, length, description, E value, bit score, query frame, query start, query end, hit start, hit end, positives, and identical # The results are tab-deliminated and ready for import into a spreadsheet program for browsing and further analysis. # use strict; use warnings; use Bio::SearchIO; # Usage information die "Usage: $0 <BLAST-report-file> <number-of-top-hits> <output-file>\n", if (@ARGV != 3); my ($infile,$numHits,$outfile) = @ARGV; print "Parsing the BLAST result ..."; my $in = Bio::SearchIO->new(-format => 'blast', -file => $infile); open (OUT,">$outfile") or die "Cannot open $outfile: $!"; # print the header info for tab-deliminated columns print OUT "query_name\tquery_length\taccession_number\tlength\tdescription\tE value\tbit score\tframe\tquery_start\t"; print OUT "query_end\thit_start\thit_end\tpositives\tidentical\n"; # extraction of information for each result recursively while ( my $result = $in->next_result ) { # the name of the query sequence print OUT $result->query_name . "\t"; # the length of the query sequence print OUT $result->query_length; # output "no hits found" if there is no hits if ( $result->num_hits == 0 ) { print OUT "\tNo hits found\n"; } else { my $count = 0; # process each hit recursively while (my $hit = $result->next_hit) { print OUT "\t" if ($count > 0); # get the accession numbers of the hits print OUT "\t" . $hit->accession . "\t"; # get the lengths of the hit sequences print OUT $hit->length . "\t"; # get the description of the hit sequences print OUT $hit->description . "\t"; # get the E value of the hit print OUT $hit->significance . "\t"; #get the bit score of the hit print OUT $hit->bits . "\t"; my $hspcount = 0; # process the top HSP for the top hit while (my $hsp = $hit->next_hsp) { print OUT "\t\t\t\t\t\t\t", if ($hspcount > 0); # get the frame of the query sequence print OUT $hsp->query->frame . "\t"; # get the start and the end of the query sequence in the alignment print OUT $hsp->start('query') . "\t" . $hsp->end('query'). "\t"; # get the start and the end of the hit sequence in the alignment print OUT $hsp->start('hit') . "\t" . $hsp->end('hit') . "\t"; # get the similarity value printf OUT "%.1f" , ($hsp->frac_conserved * 100); print OUT "%\t"; # get the identity value printf OUT "%.1f" , ($hsp->frac_identical * 100); print OUT "%\n"; $hspcount++; } $count++; # flow control for the number of hits needed last if ($count == $numHits); } } } close OUT; print " DONE!!!\n";