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#!/usr/bin/env perl
use strict;
# get the path of this script; dependencies should be in the same directory
#
my $scriptPath;
BEGIN
{
use Cwd 'abs_path';
abs_path($0) =~ /(.*)\//;
$scriptPath = $1;
}
use lib "$scriptPath/../lib";
use Krona;
if ( @ARGV < 3 )
{
print "differentiate.pl <target_taxID> <bg_taxID> <blast...>\n";
exit;
}
my ($target, $bg, @files) = @ARGV;
my @totals;
loadTaxonomy();
foreach my $file ( @files )
{
open BLAST, "<$file";
my $lastQueryID;
my $topScore;
# 0 = top hit, 1 = hit, 2 = no hit
#
my $targetHit;
my $bgHit;
while ( 1 )
{
my $line = <BLAST>;
chomp $line;
if ( $line =~ /^#/ )
{
next;
}
my
(
$queryID,
$hitID,
$identity,
$length,
$mismatches,
$gaps,
$queryStart,
$queryEnd,
$subjectStart,
$subjectEnd,
$eVal,
$bitScore
) = split /\t/, $line;
if ( $queryID ne $lastQueryID && defined $lastQueryID )
{
$totals[$bgHit][$targetHit]++;
#print "$targetHit\t$bgHit\n\n";
}
if ( ! defined $hitID )
{
last; # EOF
}
$hitID =~ /gi\|(\d+)/;
my $gi = $1;
my $taxID = getTaxID($gi);
my $name = getName($taxID);
#print "$queryID\t$taxID\t$bitScore\t$name\n";
if ( $queryID ne $lastQueryID )
{
$topScore = $bitScore;
$targetHit = 2;
$bgHit = 2;
}
if ( contains($target, $taxID) )
{
if ( $bitScore == $topScore )
{
$targetHit = 0;
}
elsif ( $targetHit == 2 )
{
$targetHit = 1;
}
}
elsif ( contains($bg, $taxID) )
{
if ( $bitScore == $topScore )
{
$bgHit = 0;
}
elsif ( $bgHit == 2 )
{
$bgHit = 1;
}
}
$lastQueryID = $queryID;
}
}
print ",,,Human\n";
print ",,top hit,hit,no hit\n";
print ",top hit,", join(',', @{$totals[0]}), "\n";
print "NHP,hit,", join(',', @{$totals[1]}), "\n";
print ",no hit,", join(',', @{$totals[2]}), "\n";
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