20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,98 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use Fasta_reader;
+
+my $usage = "usage: $0 file.fasta [kmer_length=25]\n\n";
+
+my $fasta_file = $ARGV[0] or die $usage;
+my $kmer_size = $ARGV[1] || 25;
+
+
+main: {
+
+    my $fasta_reader = new Fasta_reader($fasta_file);
+    my %trans_seqs = $fasta_reader->retrieve_all_seqs_hash();
+
+    my %acc_to_kmers = &get_kmers(\%trans_seqs);
+
+    my @accs = keys %acc_to_kmers;
+
+    
+    for (my $i = 0; $i < $#accs; $i++) {
+        
+        my $acc_i = $accs[$i];
+        my $kmers_href_i = $acc_to_kmers{$acc_i};
+
+
+        for (my $j = $i + 1; $j <= $#accs; $j++) {
+            
+            my $acc_j = $accs[$j];
+            my $kmers_href_j = $acc_to_kmers{$acc_j};
+
+            if (&have_kmer_in_common($kmers_href_i, $kmers_href_j)) {
+
+                print join("\t", $acc_i, $acc_j) . "\n";
+            }
+        }
+
+    }
+
+    exit(0);
+    
+}
+
+####
+sub get_kmers {
+    my ($trans_seqs_href) = @_;
+
+    my %acc_to_kmers;
+
+    my $counter = 0;
+    foreach my $acc (keys %$trans_seqs_href) {
+        $counter++;
+        print STDERR "-getting kmers for $counter\n";
+
+
+        my $trans_seq = $trans_seqs_href->{$acc};
+        
+        my %kmers = &extract_kmers($trans_seq);
+        $acc_to_kmers{$acc} = \%kmers;
+    }
+    
+    return(%acc_to_kmers);
+}
+
+####
+sub extract_kmers {
+    my ($seq) = @_;
+
+    my %kmers;
+
+    for (my $i = 0; $i <= length($seq) - $kmer_size; $i++) {
+        my $kmer = substr($seq, $i, $kmer_size);
+        
+        $kmers{$kmer} = 1;
+    }
+
+    return(%kmers);
+}
+
+####
+sub have_kmer_in_common {
+    my ($kmers_i, $kmers_j) = @_;
+
+    foreach my $kmer (keys %$kmers_i) {
+
+        if (exists $kmers_j->{$kmer}) {
+            return(1);
+        }
+    }
+
+    return(0);
+}
+