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#!/usr/bin/env perl
#!/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;
}
if ( @ARGV < 2 )
{
my $scriptName = getScriptName();
printHeader("KronaTools $KronaTools::version - $scriptName");
print
'Takes an ACE assembly file and writes a magnitude file for use with import
scripts. The magnitude of each contig will be the total number of reads
assigned to it.
';
printHeader('Usage');
print
"$scriptName <assembly.ace> <output>
";
exit;
}
my ($ace, $output) = @ARGV;
open ACE, "<$ace" or die $!;
open OUT, ">$output" or die $!;
while ( my $line = <ACE> )
{
if ( $line =~ /^CO\s+([^\s]+)\s+\d+\s+(\d+)/ )
{
print OUT "$1\t$2\n";
}
}
close OUT;
close ACE;
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