/usr/share/perl5/KronaTools/scripts/ImportGalaxy.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 | #!/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;
}
my @options =
qw(
out
name
combine
depth
url
postUrl
);
# set defaults
#
setOption('out', 'galaxy.krona.html');
setOption('name', 'root');
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
'Creates a Krona chart based Galaxy taxonomic representations.',
'tax_rep',
'Results from the "Fetch taxonomic representation" or "Find lowest
diagnostic rank" tools in Galaxy.',
0,
1,
\@options
);
exit 0;
}
my @ranks =
qw(
superkingdom
kingdom
subkingdom
superphylum
phylum
subphylum
superclass
class
subclass
superorder
order
suborder
superfamily
family
subfamily
tribe
subtribe
genus
subgenus
species
subspecies
);
my $tree = newTree();
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 $!;
while ( my $line = <INFILE> )
{
chomp $line;
my @lineage = split /\t/, $line;
# eat GI
#
if ( @lineage > 24 )
{
@lineage = @lineage[0..23];
}
my $queryID = shift @lineage;
my $taxID = shift @lineage;
shift @lineage; # eat root
map { if ( $_ eq 'n' ) { $_ = '' } } @lineage;
addByLineage($tree, $set, \@lineage, $queryID, undef, undef, \@ranks);
# print "$taxID : @lineage\n";
}
if ( ! getOption('combine') )
{
$set++;
}
close INFILE;
}
my @attributeNames =
(
'count',
'unassigned',
'rank',
);
my @attributeDisplayNames =
(
'Reads',
'Unassigned',
'Rank',
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames
);
|