72 lines
1.4 KiB
Perl
72 lines
1.4 KiB
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use Cwd;
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use FindBin;
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my $usage = "\n\nusage: $0 reads.fa hash_size\n\n";
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my $reads_file = $ARGV[0] or die $usage;
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my $hash_size = $ARGV[1] or die $usage;
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my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3";
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my $CPU = 4;
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my $min_kmer_cov = 1;
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unless ($reads_file =~ /^\//) {
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$reads_file = cwd() . "/$reads_file";
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}
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my $workdir = "H_" . ($hash_size/1e9) . "G";
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mkdir($workdir) or die "Error, cannot mkdir $workdir";
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chdir ($workdir) or die "Error, cannot cd to $workdir";
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my $jelly_kmer_fa_file = "jellyfish.kmers.fa";
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# my $jelly_hash_size = int( ($max_memory - $read_file_size)/7); # decided upon by Rick Westerman
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my $cmd = "$JELLYFISH_DIR/bin/jellyfish count -t $CPU -m 25 -s $hash_size ";
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# $cmd .= " --both-strands ";
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$cmd .= " $reads_file";
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&process_cmd($cmd);
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my @kmer_db_files;
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foreach my $file (<mer_counts_*>) {
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my $cmd = "$JELLYFISH_DIR/bin/jellyfish dump -L $min_kmer_cov $file >> $file.kmer_fa";
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&process_cmd($cmd);
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$cmd = "cat $file.kmer_fa >> $jelly_kmer_fa_file";
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&process_cmd($cmd);
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}
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$cmd = "grep '>' $jelly_kmer_fa_file | wc -l | tee kmer_count.txt";
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&process_cmd($cmd);
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exit(0);
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####
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sub process_cmd {
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my ($cmd) = @_;
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my $ret = system($cmd);
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if ($ret) {
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die "Error, cmd: $cmd died with ret $ret";
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}
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return;
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}
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