/usr/share/perl5/KronaTools/scripts/ImportBLAST.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 | #!/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', 'blast.krona.html');
setOption('name', 'Root');
my @options =
qw(
out
name
threshold
include
random
percentIdentity
bitScore
combine
depth
noRank
hueBad
hueGood
url
postUrl
taxonomy
factor
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
"Creates a Krona chart of taxonomic classifications computed from tabular BLAST
results.",
$KronaTools::argumentNames{'blast'},
$KronaTools::argumentDescriptions{'blast'},
1,
1,
\@options
);
exit 0;
}
my $tree = newTree();
# load taxonomy
print "Loading taxonomy...\n";
loadTaxonomy();
# parse BLAST results
my $set = 0;
my @datasetNames;
my $useMag;
foreach my $input (@ARGV)
{
my ($fileName, $magFile, $name) = parseDataset($input);
my %magnitudes;
my %taxIDs;
my %scores;
if ( ! getOption('combine') )
{
push @datasetNames, $name;
}
print "Importing $fileName...\n";
# load magnitudes
if ( defined $magFile )
{
print " Loading magnitudes from $magFile...\n";
loadMagnitudes($magFile, \%magnitudes);
$useMag = 1;
}
print " Classifying BLAST results...\n";
classifyBlast($fileName, \%taxIDs, \%scores);
print " Computing tree...\n";
foreach my $queryID ( keys %taxIDs )
{
my $taxID = $taxIDs{$queryID};
if ( $taxID == -1 )
{
if ( getOption('include') )
{
$taxID = 0;
}
else
{
next;
}
}
addByTaxID
(
$tree,
$set,
$taxID,
$queryID,
$magnitudes{$queryID},
$scores{$queryID}
);
}
if ( ! getOption('combine') )
{
$set++;
}
}
my @attributeNames =
(
'magnitude',
'magnitudeUnassigned',
'count',
'unassigned',
'taxon',
'rank',
'score'
);
my @attributeDisplayNames =
(
$useMag ? 'Magnitude' : undef,
$useMag ? 'Unassigned magnitude' : undef,
'Count',
'Unassigned',
'Tax ID',
'Rank',
getScoreName(),
);
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
getOption('bitScore') || getOption('percentIdentity') ?
getOption('hueBad') :
getOption('hueGood'),
getOption('bitScore') || getOption('percentIdentity') ?
getOption('hueGood') :
getOption('hueBad')
);
|