/usr/share/perl5/KronaTools/scripts/GetContigMagnitudesCONTIG.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 | #!/usr/bin/env perl
# Copyright 2011 Brian Ondov
#
# This file is part of Radiant.
#
# Radiant is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Radiant is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Radiant. If not, see <http://www.gnu.org/licenses/>.
use strict;
if ( @ARGV < 2 )
{
print '
ktGetContigMagnitudesCONTIG <assembly.contig> <output>
Writes a magnitude file for use with import scripts. The magnitude of each
contig will be the total number of reads assigned to it.
';
exit;
}
my ($contig, $output) = @ARGV;
open CONTIG, "<$newblerFolder/454ContigGraph.txt" or die $!;
open OUT, ">$output" or die $!;
while ( my $line = <CONTIG> )
{
if ( $line =~ /^C/ )
{
last;
}
else
{
my @values = split /\t/, $line;
my $magnitude = $values[2] * $values[3];
print OUT "$values[1]\t$magnitude\n";
}
}
close OUT;
close CONTIG;
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