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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('name', 'all');
setOption('out', 'mg-rast.krona.html');
my @options =
qw(
out
name
combine
depth
hueBad
hueGood
percentIdentity
url
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
'Creates a Krona chart from MG-RAST organism or functional analyses.',
'mgrast_table',
'A table exported from MG-RAST. It can be from organism or functional
analysis, but all tables being imported should be consistent.',
0,
1,
\@options
);
exit 0;
}
my $tree = newTree();
my @ranks;
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 $!;
my $header = <INFILE>;
my $offset;
my @fields = split /\t/, $header;
# remove metagenome and source (if present)
#
shift @fields;
#
if ( $fields[0] eq 'source' )
{
shift @fields;
$offset = 2;
}
else
{
$offset = 1;
}
my $i = 0;
while ( $fields[0] ne 'abundance' )
{
$ranks[$i] = shift @fields;
$i++;
}
while ( my $line = <INFILE> )
{
chomp $line;
my @data = split /\t/, $line;
my $magnitude = $data[$offset + @ranks];
my $score;
my @lineage = @data[$offset..($offset + @ranks - 1)];
map { if ( $_ eq '-' ) { $_ = '' } } @lineage;
if ( getOption('percentIdentity') )
{
$score = $data[$offset + 2 + @ranks];
}
else
{
$score = $data[$offset + 1 + @ranks];
}
addByLineage($tree, $set, \@lineage, undef, $magnitude, $score, \@ranks);
}
close INFILE;
if ( ! getOption('combine') )
{
$set++;
}
}
my @attributeNames =
(
'magnitude',
'magnitudeUnassigned',
'score',
'rank'
);
my @attributeDisplayNames =
(
'Abundance',
'Unassigned',
getScoreName(),
'Rank'
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
getOption('percentIdentity') ? getOption('hueBad') : getOption('hueGood'),
getOption('percentIdentity') ? getOption('hueGood') : getOption('hueBad')
);
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