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
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
|
#!/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', 'root');
setOption('out', 'rdp.comp.krona.html');
# Prevent the magnitude and score of each classification from being added to its
# ancestors. This is necessary because internal nodes are explicitly listed in
# the RDP comparison results.
#
setOption('leafAdd', 1);
my @options =
qw(
out
name
depth
hueBad
hueGood
url
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
my $scriptName = getScriptName();
printHeader("KronaTools $KronaTools::version - $scriptName");
print
'Creates a Krona chart from an RDP library comparison.
';
printHeader('Usage');
print
"$scriptName [options] rdp_comparison [name1] [name2]
";
printColumns
(
' rdp_comparison',
'RDP comparison result downloaded as text.',
' name',
'A name for each library to appear in the chart. The default is "Library
[1/2]".',
);
printOptions(@options);
exit 0;
}
my @ranks =
(
'Domain',
'Phylum',
'Class',
'Order',
'Family',
'Genus',
);
my $tree = newTree();
my ($fileName, $name1, $name2) = @ARGV;
if ( ! defined $name1 )
{
$name1 = 'Library 1';
$name2 = 'Library 2';
}
my @datasetNames = ($name1, $name2);
my @lineage;
my @scores;
my $minScores;
print "Importing $fileName...\n";
open INFILE, "<$fileName" or die $!;
my $line;
do
{
$line = <INFILE>;
if ( ! $line )
{
ktDie("\"$fileName\" is not RDP comparison file.");
}
}
while ( <INFILE> !~ /^Rank/ );
while ( my $line = <INFILE> )
{
chomp $line;
my ($rank, $lineageString, $taxon, $mag1, $mag2, $score) = split / \| /, $line;
if ( $taxon )
{
my @lineage = split /"?;"?/, $lineageString;
if ( substr($taxon, 0, 1) eq '"' && substr($taxon, -1, 1) eq '"' )
{
$taxon = substr($taxon, 1);
chop $taxon;
}
$taxon =~ s/"/"/g;
my @scores;
if ( $rank ) # no rank means unclassified, so no score
{
push @lineage, $taxon;
shift @lineage; # remove root
if ( $score )
{
$score = log $score;
}
else
{
$score = $KronaTools::minEVal;
$minScores++;
}
addByLineage($tree, 0, \@lineage, undef, $mag1, $score);
addByLineage($tree, 1, \@lineage, undef, $mag2, $score);
}
}
}
close INFILE;
if ( $minScores)
{
print "\nWarning: Couldn't log[10] of 0 for $minScores scores. Approximated as $KronaTools::minEVal.\n\n";
}
my @attributeNames =
(
'magnitude',
'score'
);
my @attributeDisplayNames =
(
'Abundance',
'Log significance'
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
getOption('hueGood'),
getOption('hueBad')
);
|
