/usr/share/perl5/KronaTools/scripts/ClassifyBLAST_hash.pl is in radiant 2.7+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# Copyright © 2011, Battelle National Biodefense Institute (BNBI);
# all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and
# Adam Phillippy
#
# See the LICENSE.txt file included with this software for license information.
use strict;
# get the path of this script; dependencies are relative
#
my $scriptPath;
BEGIN
{
use Cwd 'abs_path';
abs_path($0) =~ /(.*)\//;
$scriptPath = $1;
}
use lib "$scriptPath/../lib";
use Krona;
my $totalMag;
my @options =
qw(
out
radius
verbose
);
setOption('out', 'blast.taxonomy.tab');
setOption('radius', 0);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
print '
Description:
Infers taxonomic abundance from BLAST results.
Usage:
ktClassifyBLAST [options] \
blast_output_1[:magnitude_file_1] \
blast_output_2[:magnitude_file_2] \
...
Input:
blast_output File containing BLAST results in tabular format ("Hit table
(text)" when downloading from NCBI). If running BLAST
locally, subject IDs in the local database must contain GI
numbers in "gi|12345" format.
[magnitude_file] Optional file listing query IDs with magnitudes, separated
by tabs. The can be used to account for read length or
contig depth to obtain a more accurate representation of
abundance. By default, query sequences without specified
magnitudes will be assigned a magnitude of 1. Magnitude
files for Newbler or Celera Assembler assemblies can be
created with getContigMagnitudesNewbler.pl or
getContigMagnitudesCA.pl
';
printOptions(@options);
exit;
}
my %bestScores;
my %lca;
my %lcaMag;
# load taxonomy
print "Loading taxonomy...\n";
loadTaxonomy();
# parse BLAST results
foreach my $input (@ARGV)
{
my ($fileName, $magFile) = split /:/, $input;
$fileName =~ /([^\/]+)\./;
my %magnitudes;
# load magnitudes
if ( defined $magFile )
{
print "Loading magnitudes for $fileName...\n";
open MAG, "<$magFile" or die $!;
while ( my $line = <MAG> )
{
chomp $line;
my ( $id, $mag ) = split /\t/, $line;
$magnitudes{$id} = $mag;
}
close MAG;
}
print "Classifying $fileName...\n";
open BLAST, "<$fileName";
my $lastQueryID;
my $topScore;
my $taxID;
my $score;
while ( my $line = <BLAST> )
{
if ( $line =~ /^#/ )
{
next;
}
chomp $line;
my
(
$queryID,
$hitID,
$identity,
$length,
$mismatches,
$gaps,
$queryStart,
$queryEnd,
$subjectStart,
$subjectEnd,
$eVal,
$bitScore
) = split /\t/, $line;
$hitID =~ /gi\|(\d+)/;
my $gi = $1;
my $bestScore = $bestScores{$queryID};
#print "$queryID\t$bestScore\n";
if
(
defined $gi &&
(
! defined $bestScore ||
$bitScore >= $bestScore - getOption('radius')
)
)
{
if
(
! defined $bestScore ||
$bitScore > $bestScore
)
{
$bestScores{$queryID} = $bitScore
}
my $taxID = getTaxID($gi);
if ( defined $lca{$queryID} )
{
$lca{$queryID} = lowestCommonAncestor($lca{$queryID}, $taxID);
}
else
{
$lca{$queryID} = $taxID;
}
if ( defined $magnitudes{$lastQueryID} )
{
$lcaMag{$queryID} = $magnitudes{$queryID};
}
else
{
$lcaMag{$queryID} = 1;
}
}
}
}
my %totalMagnitudes;
my %totalScores;
my %totalCounts;
print "Computing taxon totals...\n";
foreach my $query ( keys %lca )
{
# add the chosen hit from the last queryID
my $taxID = $lca{$query};
if ( getOption('verbose') )
{
print "$query:\ttaxID=$taxID\tmag=$lcaMag{$query}\tscore=$bestScores{$query}\n";
}
#add($set, \%tree, $taxID, $magnitude, $score);
$totalMagnitudes{$taxID} += $lcaMag{$query};
$totalScores{$taxID} += $bestScores{$query};
$totalCounts{$taxID}++;
}
my $outFile = getOption('out');
print "Writing $outFile...\n";
open OUT, ">$outFile" or die "Could not open $outFile for writing";
foreach my $taxID ( keys %totalMagnitudes )
{
my $score = $totalScores{$taxID} / $totalCounts{$taxID};
print OUT "$taxID\t$totalMagnitudes{$taxID}\t$score\n";
}
close OUT;
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