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#!/usr/bin/env perl
# 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;
BEGIN
{
use File::Basename;
use Cwd 'abs_path';
use lib dirname(abs_path($0)) . "/../lib";
use KronaTools;
}
# defaults
#
setOption('out', 'blast.krona.html');
setOption('name', 'Root');
my @options =
qw(
out
name
threshold
include
random
percentIdentity
bitScore
combine
depth
noRank
hueBad
hueGood
url
postUrl
taxonomy
factor
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
"Creates a Krona chart of taxonomic classifications computed from tabular BLAST
results.",
$KronaTools::argumentNames{'blast'},
$KronaTools::argumentDescriptions{'blast'},
1,
1,
\@options
);
exit 0;
}
my $tree = newTree();
# load taxonomy
print "Loading taxonomy...\n";
loadTaxonomy();
# parse BLAST results
my $set = 0;
my @datasetNames;
my $useMag;
foreach my $input (@ARGV)
{
my ($fileName, $magFile, $name) = parseDataset($input);
my %magnitudes;
my %taxIDs;
my %scores;
if ( ! getOption('combine') )
{
push @datasetNames, $name;
}
print "Importing $fileName...\n";
# load magnitudes
if ( defined $magFile )
{
print " Loading magnitudes from $magFile...\n";
loadMagnitudes($magFile, \%magnitudes);
$useMag = 1;
}
print " Classifying BLAST results...\n";
classifyBlast($fileName, \%taxIDs, \%scores);
print " Computing tree...\n";
foreach my $queryID ( keys %taxIDs )
{
my $taxID = $taxIDs{$queryID};
if ( $taxID == -1 )
{
if ( getOption('include') )
{
$taxID = 0;
}
else
{
next;
}
}
addByTaxID
(
$tree,
$set,
$taxID,
$queryID,
$magnitudes{$queryID},
$scores{$queryID}
);
}
if ( ! getOption('combine') )
{
$set++;
}
}
my @attributeNames =
(
'magnitude',
'magnitudeUnassigned',
'count',
'unassigned',
'taxon',
'rank',
'score'
);
my @attributeDisplayNames =
(
$useMag ? 'Magnitude' : undef,
$useMag ? 'Unassigned magnitude' : undef,
'Count',
'Unassigned',
'Tax ID',
'Rank',
getScoreName(),
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
getOption('bitScore') || getOption('percentIdentity') ?
getOption('hueBad') :
getOption('hueGood'),
getOption('bitScore') || getOption('percentIdentity') ?
getOption('hueGood') :
getOption('hueBad')
);
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