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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
use List::Util qw(min max);
my $usage = "\n\n\tusage: $0 blast.outfmt6 query_fasta target_fasta\n";
my $blast_file = $ARGV[0] or die $usage;
my $query_fasta = $ARGV[1] or die $usage;
my $target_fasta = $ARGV[2] or die $usage;
main: {
my %query_seq_lens = &get_seq_lengths($query_fasta);
my %target_seq_lens;
if ($query_fasta eq $target_fasta) {
%target_seq_lens = %query_seq_lens;
}
else {
%target_seq_lens = &get_seq_lengths($target_fasta);
}
open (my $fh, $blast_file) or die "Error, cannot open file $blast_file";
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $query_acc = $x[0];
my $target_acc = $x[1];
my $query_len = $query_seq_lens{$query_acc} or die "Error, cannot find seq length for query: $query_acc";
my $target_len = $target_seq_lens{$target_acc} or die "Error, cannot find seq length for target: $target_acc";
my $query_hit_len = abs($x[7]-$x[6]);
my $db_hit_len = abs($x[9]-$x[8]);
my $pct_query_len = sprintf("%.2f", $query_hit_len / $query_len * 100);
my $pct_target_len = sprintf("%.2f", $db_hit_len / $target_len * 100);
push (@x, $query_len, $pct_query_len, $target_len, $pct_target_len, max($pct_query_len, $pct_target_len));
print join("\t", @x) . "\n";
}
exit(0);
}
####
sub get_seq_lengths {
my ($fasta_file) = @_;
my %seq_lens;
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $seq_len = length($seq_obj->get_sequence());
$seq_lens{$acc} = $seq_len;
}
return(%seq_lens);
}
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