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#!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
use FindBin;
my $usage = "\n\nusage: $0 reads.fa hash_size\n\n";
my $reads_file = $ARGV[0] or die $usage;
my $hash_size = $ARGV[1] or die $usage;
my $JELLYFISH_DIR = "/usr";
my $CPU = 4;
my $min_kmer_cov = 1;
unless ($reads_file =~ /^\//) {
$reads_file = cwd() . "/$reads_file";
}
my $workdir = "H_" . ($hash_size/1e9) . "G";
mkdir($workdir) or die "Error, cannot mkdir $workdir";
chdir ($workdir) or die "Error, cannot cd to $workdir";
my $jelly_kmer_fa_file = "jellyfish.kmers.fa";
# my $jelly_hash_size = int( ($max_memory - $read_file_size)/7); # decided upon by Rick Westerman
my $cmd = "$JELLYFISH_DIR/bin/jellyfish count -t $CPU -m 25 -s $hash_size ";
# $cmd .= " --both-strands ";
$cmd .= " $reads_file";
&process_cmd($cmd);
my @kmer_db_files;
foreach my $file (<mer_counts_*>) {
my $cmd = "$JELLYFISH_DIR/bin/jellyfish dump -L $min_kmer_cov $file >> $file.kmer_fa";
&process_cmd($cmd);
$cmd = "cat $file.kmer_fa >> $jelly_kmer_fa_file";
&process_cmd($cmd);
}
$cmd = "grep '>' $jelly_kmer_fa_file | wc -l | tee kmer_count.txt";
&process_cmd($cmd);
exit(0);
####
sub process_cmd {
my ($cmd) = @_;
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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