/usr/share/perl5/KronaTools/scripts/getContigMagnitudesCA.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 | #!/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 '
getContigMagnitudesCA.pl <assembly_folder> <output>
Writes a magnitude file for use with import scripts. The magnitude of each
contig will be the total number of bases assigned to it (also equal to
depth * length).
';
exit;
}
my ($wgsFolder, $output) = @ARGV;
my ($frgctgFile) = glob "$wgsFolder/9-terminator/*.posmap.frgctg";
my %contigMagnitudes;
open POSMAP, "<$frgctgFile" or die $!;
while ( my $line = <POSMAP> )
{
my ($read, $contigID, $start, $end, $strand) = split /\t/, $line;
my $contigName = 'ctg' . $contigID;
$contigMagnitudes{$contigName} += $end - $start + 1;
}
close POSMAP;
open OUT, ">$output" or die $!;
foreach my $contig ( keys %contigMagnitudes )
{
print OUT "$contig\t$contigMagnitudes{$contig}\n";
}
close OUT;
|