/usr/share/perl5/KronaTools/scripts/ImportEC.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.
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# 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', 'ec.krona.html');
setOption('name', 'root');
my @options =
qw(
out
name
combine
queryCol
ecCol
scoreCol
magCol
include
depth
hueBad
hueGood
url
postUrl
);
getKronaOptions(@options);
if
(
@ARGV < 1
)
{
printUsage
(
'Creates a Krona chart of abundances of EC (Enzyme Commission) numbers
in tab-delimited files.',
'ec_numbers',
'Tab-delimited files with EC numbers and (optionally) query IDs,
magnitudes and scores. By default, query IDs, EC numbers and scores will be
taken from columns 1, 2 and 3, respectively (see -q, -e, -s, and -m).',
1,
1,
\@options
);
exit 0;
}
if ( optionsConflict('queryCol', 'ecCol', 'magCol', 'scoreCol') )
{
ktWarn('Query column already in use; not reading query IDs.');
setOption('queryCol', undef);
}
if ( optionsConflict('scoreCol', 'ecCol', 'magCol') )
{
ktWarn('Score column already in use; not reading scores.');
setOption('scoreCol', undef);
}
if ( optionsConflict('magCol', 'ecCol') )
{
ktWarn('Magnitude column already in use; not reading magnitudes.');
setOption('magCol', undef);
}
my $tree = newTree();
print "Loading EC names...\n";
loadEC();
my $set = 0;
my @datasetNames;
my $useScore = 1; # is score column present?
my $eVal; # is score e-value (inferred by negative scores)?
my $useMag = getOption('magCol'); # using magnitude values?
foreach my $input (@ARGV)
{
my ($file, $magFile, $name) = parseDataset($input);
my %magnitudes;
if ( ! getOption('combine') )
{
push @datasetNames, $name;
}
print "Importing $file...\n";
# load magnitudes
if ( defined $magFile )
{
if ( getOption('queryCol') )
{
print " Loading magnitudes from $magFile...\n";
loadMagnitudes($magFile, \%magnitudes);
$useMag = 1;
}
else
{
ktWarn("Query column not defined; not reading magnitudes from \"$magFile.\"");
}
}
open IN, "<$file" or die "Couldn't open $file.";
while ( my $line = <IN> )
{
my @fields = split /\t/, $line;
my $queryID;
my $ec = $fields[getOption('ecCol') - 1];
my $magnitude;
my $score;
if ( getOption('queryCol') )
{
$queryID = $fields[getOption('queryCol') - 1];
}
if ( getOption('scoreCol') )
{
$score = $fields[getOption('scoreCol') - 1];
}
if ( defined $queryID && defined $magnitudes{$queryID} )
{
$magnitude = $magnitudes{$queryID};
}
elsif ( defined getOption('magCol') )
{
$magnitude = $fields[getOption('magCol') - 1];
}
else
{
$magnitude = 1;
}
$ec =~ s/^EC//; # remove 'EC' if present
while ( $ec =~ s/\.-$// ) {}; # repeatedly remove trailing '.-'
if ( $ec ne '' && $ec !~ /^[\d\.]+$/ )
{
ktWarn("$queryID: Bad EC ('$ec'); ignoring.");
$ec = '';
}
if ( $ec || getOption('include') )
{
my @ecs;
if ( $ec )
{
@ecs = split /\./, $ec;
}
addByEC($tree, $set, \@ecs, $queryID, $magnitude, $score);
}
if ( ! defined $score ) # all lines must have score to be used
{
$useScore = 0;
}
if ( $score < 0 ) # score is probably e-value; flip colors
{
$eVal = 1;
}
}
if ( ! getOption('combine') )
{
$set++;
}
close IN;
}
my @attributeNames =
(
'magnitude',
'count',
'unassigned',
'ec',
);
my @attributeDisplayNames =
(
$useMag ? 'Magnitude' : (getOption('queryCol') ? undef : 'Count'),
getOption('queryCol') ? 'Count' : undef,
'Unassigned',
'EC'
);
my @scoreArgs;
if ( $useScore )
{
push @attributeNames, 'score';
push @attributeDisplayNames, 'Avg. score';
@scoreArgs =
(
$eVal ? getOption('hueGood') : getOption('hueBad'),
$eVal ? getOption('hueBad') : getOption('hueGood')
)
}
writeTree
(
$tree,
\@attributeNames,
\@attributeDisplayNames,
\@datasetNames,
@scoreArgs
);
sub optionsConflict
{
my ($option, @others) = @_;
if ( getOption($option) )
{
foreach my $other ( @others )
{
if ( getOption($option) == getOption($other) )
{
return 1;
}
}
}
return 0;
}
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