20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,71 @@
+#!/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 = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3";
+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;
+}
+
+