/usr/share/perl5/KronaTools/scripts/ImportMGRAST.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | #!/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')
);
|