/
get_kmer_frequencies4.pl
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/
get_kmer_frequencies4.pl
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#!/usr/bin/perl
###########################################################################
### Get kmer Frequencies ###
### Usage: get_kmer_frequencies.pl <fasta file> ###
### This program takes a fasta file, k and a prefix as it's parameters. ###
### ###
### It returns a tab delimited file ###
### ###
### Jennifer Meneghin ###
### May 11, 2015 ###
### ###
### Updated. Now it returns results with summed reverse compliments ###
### Jennifer Meneghin ###
### February 10, 2016 ###
###########################################################################
#
# Output identical to original jmeneghin/get_kmer_frequencies.pl - duffee, July 2023
#
#---------------------------------------------------------------------------------------------------------------------------
#Deal with passed parameters
#---------------------------------------------------------------------------------------------------------------------------
use warnings;
use strict;
use v5.10;
usage() unless @ARGV;
my ($fasta_file, $k, $prefix) = @ARGV;
my $out_file = "${prefix}_kmers.txt";
open my $in_fh, '<', $fasta_file or die "Got a bad fasta file: $fasta_file : $!\n";
open my $out_fh, '>', $out_file or die "Couldn't create $out_file: $!\n";
say join "\n", "Parameters:", "fasta file = $fasta_file", "output file = $out_file",
"k = $k";
#---------------------------------------------------------------------------------------------------------------------------
#The main event
#---------------------------------------------------------------------------------------------------------------------------
my $start = time();
my ($seq, $id, %knucs) = (0, 0, ());
my ($pc, $linecount) = (0, 0);
while (<$in_fh>) {
chomp;
if (/^>/) {
#finish up previous line.
if (length($seq) > 0) {
process_it();
}
#start new line.
$id = $_;
$id =~ s/^>//g;
$pc++;
if ($pc % 100 == 0) {
say "count = $pc";
}
} else {
$seq .= uc($_);
}
$linecount++;
if ($linecount % 10000 == 0) {
say "line count = $linecount";
}
}
#finish up last line.
process_it();
say "Sorting...";
my (%kmers, %records);
for my $i (keys %knucs) {
my ($record, $kmer) = split ':', $i;
$kmers{$kmer}++;
$records{$record}++;
}
my @record_keys = sort keys %records;
say "Printing...";
say $out_fh join "\t", "${k}-mer", @record_keys; # header line
my $testsum = 0;
for my $i (sort keys %kmers) {
my @items = map { my $key = join ':', $_, $i; $knucs{$key} // 0 }
@record_keys;
say $out_fh join "\t", $i, @items;
# $testsum += $_ for @items;
}
#print "TEST SUM = $testsum\n";
close($in_fh);
close($out_fh);
my $stop = time();
my $total_time = $stop - $start;
say "Total time to run = $total_time";
exit;
sub usage {
say <<USAGE;
Get kmer Frequencies
Usage: $0 <fasta file>
This program takes a fasta file, k and prefix as it's parameters.
It returns a tab delimited file (knucs_out.txt) of kmer counts. (columns = records, rows = kmer counts.)
Jennifer Meneghin
May 11, 2015
Updated. Now results are returned with summed reverse compliments
Jennifer Meneghin
February 10, 2016
USAGE
exit;
}
sub process_it {
my @letters = split //, $seq;
my $end = @letters - $k;
for my $i (0 .. $end) {
my $thiskmer = q{};
for my $j ($i .. ($i + $k - 1)) {
$thiskmer .= $letters[$j];
}
my $rckmer = rc_seq($thiskmer);
#print "$id\tthiskmer = $thiskmer\n";
#print "$id\trc kmer = $rckmer\n";
my $key = join ':', $id, ($thiskmer le $rckmer ? $thiskmer : $rckmer);
$knucs{$key}++;
}
$seq = q{};
$id = q{};
}
sub rc_seq {
my ($mykmer) = @_;
my @myletters = split //, $mykmer;
my (@rcmykmer, $thisrcmykmer);
for my $i (0 .. $k - 1) {
if ($myletters[$i] eq "A") {
$rcmykmer[ $k - $i - 1 ] = "T";
} elsif ($myletters[$i] eq "C") {
$rcmykmer[ $k - $i - 1 ] = "G";
} elsif ($myletters[$i] eq "G") {
$rcmykmer[ $k - $i - 1 ] = "C";
} elsif ($myletters[$i] eq "T") {
$rcmykmer[ $k - $i - 1 ] = "A";
} else {
$rcmykmer[ $k - $i - 1 ] = $myletters[$i]; #No swap of Ns and such
}
}
$thisrcmykmer = join q{}, map { $rcmykmer[$_] } (0 .. $k - 1);
return $thisrcmykmer;
}