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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;
}
setOption('out', 'fcp.krona.html');
setOption('name', 'root');
my @options =
qw(
out
name
combine
depth
url
postUrl
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
'Creates a Krona chart based on the results of FCP (Fragment Classification
Package).',
'fcp_output',
'Results of running any FCP classification tool (except BLASTN.py, which only
outputs raw BLAST results).',
1,
1,
\@options
);
exit 0;
}
my $tree = newTree();
my @datasetNames;
my $set = 0;
my $useMag;
foreach my $input ( @ARGV )
{
my ($fileName, $magFile, $name) = parseDataset($input);
if ( ! getOption('combine') )
{
push @datasetNames, $name;
}
my %magnitudes;
my $totalMagnitude;
if ( defined $magFile )
{
print " Loading magnitudes from $magFile...\n";
loadMagnitudes($magFile, \%magnitudes);
$useMag = 1;
}
print " Reading classifications from $fileName...\n";
open INFILE, "<$fileName" or die $!;
<INFILE>; # eat header
while ( my $line = <INFILE> )
{
chomp $line;
my ($readID, $classification) = split /\t/, $line;
my @lineage = split /;/, $classification;
my $magnitude = 1;
if ( %magnitudes )
{
if ( defined $magnitudes{$readID} )
{
$magnitude = $magnitudes{$readID};
}
else
{
ktWarn("Query ID \"$readID\" doesn't exist in magnitude file; using 1.");
}
}
addByLineage($tree, $set, \@lineage, $readID, $magnitude);
}
if ( ! getOption('combine') )
{
$set++;
}
close INFILE;
}
my @attributeNames =
(
'magnitude',
'magnitudeUnassigned',
'count',
'unassigned'
);
my @attributeDisplayNames =
(
$useMag ? 'Magnitude' : undef,
$useMag ? 'Unassigned magnitude' : undef,
'Count',
'Unassigned'
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
);
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