20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,47 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Carp;
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use Fasta_reader;
+use Ktree;
+use Nuc_translator;
+
+my $usage = "usage: $0 fasta_file KmerSize [DSmode]\n\n";
+
+my $fasta_file = $ARGV[0] or die $usage;
+my $kmer_length = $ARGV[1] or die $usage;
+my $DS_mode = $ARGV[2] || 0;
+
+
+main: {
+    
+    my $ktree = new Ktree();
+
+    my $fasta_reader = new Fasta_reader($fasta_file);
+    while (my $seq_obj = $fasta_reader->next()) {
+        
+        my $seq = $seq_obj->get_sequence();
+        my @chars = split(//, $seq);
+
+        for (my $i = 0; $i <= length($seq) - $kmer_length; $i++) {
+            
+            my $kmer = join("", @chars[$i..($i+$kmer_length-1)]);
+            
+            $ktree->add_kmer($kmer);
+            
+            if ($DS_mode) {
+                $ktree->add_kmer( &reverse_complement($kmer) );
+            }
+        }
+    }
+    
+    $ktree->report_kmer_counts();
+    
+    exit(0);
+}
+
+
+