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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;
}
my @options =
qw(
out
name
combine
depth
url
postUrl
);
# set defaults
#
setOption('out', 'galaxy.krona.html');
setOption('name', 'root');
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
'Creates a Krona chart based Galaxy taxonomic representations.',
'tax_rep',
'Results from the "Fetch taxonomic representation" or "Find lowest
diagnostic rank" tools in Galaxy.',
0,
1,
\@options
);
exit 0;
}
my @ranks =
qw(
superkingdom
kingdom
subkingdom
superphylum
phylum
subphylum
superclass
class
subclass
superorder
order
suborder
superfamily
family
subfamily
tribe
subtribe
genus
subgenus
species
subspecies
);
my $tree = newTree();
my @datasetNames;
my $set = 0;
foreach my $input ( @ARGV )
{
my ($fileName, $magFile, $name) = parseDataset($input);
if ( ! getOption('combine') )
{
push @datasetNames, $name;
}
print "Importing $fileName...\n";
open INFILE, "<$fileName" or die $!;
while ( my $line = <INFILE> )
{
chomp $line;
my @lineage = split /\t/, $line;
# eat GI
#
if ( @lineage > 24 )
{
@lineage = @lineage[0..23];
}
my $queryID = shift @lineage;
my $taxID = shift @lineage;
shift @lineage; # eat root
map { if ( $_ eq 'n' ) { $_ = '' } } @lineage;
addByLineage($tree, $set, \@lineage, $queryID, undef, undef, \@ranks);
# print "$taxID : @lineage\n";
}
if ( ! getOption('combine') )
{
$set++;
}
close INFILE;
}
my @attributeNames =
(
'count',
'unassigned',
'rank',
);
my @attributeDisplayNames =
(
'Reads',
'Unassigned',
'Rank',
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames
);
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