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
|
#!/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;
}
# defaults
#
setOption('out', 'krona.krona.html');
setOption('hueBad', undef);
setOption('hueGood', undef);
setOption('name', undef);
my @options =
qw(
out
name
combine
depth
hueBad
hueGood
url
postUrl
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
"Creates a Krona chart from the data in other Krona charts.",
"krona_chart",
"Krona HTML file created with KronaTools or the Krona Excel Template",
1,
1,
\@options
);
exit 0;
}
my $tree = newTree();
my $dataset = 0;
my $nodeID = 0;
my @attributeNames;
my @attributeDisplayNames;
my %attributeDisplayByNames;
my @datasetNames;
my $line;
foreach my $input (@ARGV)
{
print "Reading $input...\n";
open XML, $input or die "Could not open $input";
while ( $line !~ /<krona/ )
{
$line = <XML>;
}
while ( $line = <XML> )
{
if ( $line =~ /<attribute display="([^"]+)".*>([^<]+)<\/attribute>/ )
{
if ( $dataset == 0 )
{
push @attributeNames, $2;
push @attributeDisplayNames, $1;
$attributeDisplayByNames{$2} = $1;
}
elsif ( ! $attributeDisplayByNames{$2} || $attributeDisplayByNames{$2} ne $1 )
{
ktDie("$input is not compatible with the first chart (\"$ARGV[0]\")");
}
}
elsif ( $line =~ /<dataset>([^<]+)<\/dataset>/ )
{
push @datasetNames, $1;
}
elsif ( $line =~ /<color attribute="score" hueStart="(\d+)" hueEnd="(\d+)"/ )
{
if ( ! defined getOption('hueBad') )
{
setOption('hueBad', $1);
}
if ( ! defined getOption('hueGood') )
{
setOption('hueGood', $2);
}
}
elsif ( $line =~ /<node name="([^"]*)"/ )
{
if ( $dataset == 0 && ! defined getOption('name') )
{
setOption('name', $1);
}
addXML($tree, \*XML, $dataset, $input);
}
}
close XML;
$dataset = @datasetNames;
}
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
getOption('hueBad'),
getOption('hueGood')
);
|
