/usr/share/perl5/KronaTools/scripts/ImportMETAREP-blast.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 | #!/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('out', 'metarep-blast.krona.html');
setOption('name', 'root');
my @options =
qw(
out
name
random
percentIdentity
bitScore
combine
depth
noRank
hueBad
hueGood
url
postUrl
taxonomy
verbose
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
'Creates a Krona chart by classifying reads based on BLAST results in METAREP
data folders.',
$KronaTools::argumentNames{'metarep'},
$KronaTools::argumentDescriptions{'metarep'},
0,
1,
\@options
);
exit 0;
}
my $tree = newTree();
print "Loading taxonomy...\n";
loadTaxonomy();
my $lastReadID;
my $set = 0;
my @datasetNames;
my $zeroEVal;
foreach my $input (@ARGV)
{
my ($folder, $magFile, $name) = parseDataset($input);
if ( ! getOption('combine') )
{
push @datasetNames, $name;
}
print "Importing $folder...\n";
if ( -e "$folder/blast.tab" )
{
open IN, "<$folder/blast.tab" or
ktDie("Couldn't open blast file in $folder");
}
else
{
open IN, "gunzip -c $folder/blast.tab.gz |" or
ktDie("Couldn't open gzipped blast file in $folder.");
}
while ( my $line = <IN> )
{
chomp $line;
my @values = split /\t/, $line;
my $readID = $values[0];
if ( $readID ne $lastReadID )
{
my $ties = 0;
my %lcaSet;
my @randomArray;
my $taxID;
my $readLength = $values[2];
while ( $values[15] =~ /taxon:(\d+)/g )
{
my $newTaxID = $1;
if ( ! taxIDExists($newTaxID) )
{
ktWarn("$readID: Taxon $newTaxID does not exist; using root.\n");
$newTaxID = 1;
}
if ( getOption('random') )
{
push @randomArray, $newTaxID;
}
else
{
$lcaSet{$newTaxID} = 1;
}
}
if ( getOption('random') )
{
$taxID = $randomArray[int(rand(scalar @randomArray))];
}
else
{
$taxID = taxLowestCommonAncestor(keys %lcaSet);
}
if ( getOption('verbose') )
{
print "$readID\ttaxID: $taxID\n";
}
my $score;
if ( getOption('percentIdentity') )
{
$score = $values[11];
}
elsif ( getOption('bitScore') )
{
$score = $values[12];
}
else
{
if ( $values[19] > 0 )
{
$score = log $values[19];
}
else
{
$score = $KronaTools::minEVal;
$zeroEVal = 1;
}
}
addByTaxID($tree, $set, $taxID, $readID, undef, $score);
}
$lastReadID = $readID;
}
if ( ! getOption('combine') )
{
$set++;
}
close IN;
}
if ( $zeroEVal )
{
ktWarn("Couldn't take base-10 log for e-values of 0. Approximated as $KronaTools::minEval.");
}
my @attributeNames =
(
'count',
'unassigned',
'taxon',
'rank',
'score',
);
my @attributeDisplayNames =
(
'Peptides',
'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')
);
|