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#!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
use Nuc_translator;
my $usage = "usage:\t $0 refTrans.fasta [strandSpecific=0]\n\n";
my $trans_fa = $ARGV[0] or die $usage;
my $strand_specific_flag = $ARGV[1] or 0;
my $kmer_size = 24;
main: {
my %kmer_to_gene;
my $counter = 0;
my $fasta_reader = new Fasta_reader($trans_fa);
while (my $seq_obj = $fasta_reader->next()) {
my $accession = $seq_obj->get_accession();
my $sequence = uc $seq_obj->get_sequence();
$counter++;
print STDERR "\r[$counter] -tracking $accession";
my ($trans, $gene) = split(/;/, $accession);
unless ($gene) {
die "Error, need format: >trans;gene , instead found: $accession ";
}
for (my $i = 0; $i <= length($sequence) - $kmer_size; $i++) {
my $kmer = substr($sequence, $i, $kmer_size);
unless (length($kmer) == $kmer_size) {
die "Error, didn't extract proper kmer length $kmer_size : [$kmer] ";
}
unless ($strand_specific_flag) {
my @kmers = ($kmer, &reverse_complement($kmer));
@kmers = sort @kmers;
$kmer = $kmers[0];
}
$kmer_to_gene{$kmer}->{$gene} = 1;
}
}
print STDERR "\n\n-reorganizing as gene sets to kmer lists.\n";
my %genes_to_kmers;
foreach my $kmer (keys %kmer_to_gene) {
my @genes = keys %{$kmer_to_gene{$kmer}};
if (scalar @genes > 1) {
my $gene_token = join(",", sort @genes);
push (@{$genes_to_kmers{$gene_token}}, $kmer);
}
}
print STDERR "\n\n-outputting gene links and kmers.\n";
foreach my $gene_set (sort keys %genes_to_kmers) {
my @kmers = sort @{$genes_to_kmers{$gene_set}};
print "$gene_set\t" . join(",", sort @kmers) . "\n";
}
exit(0);
}
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