/
get_kmer_frequencies_original.pl
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get_kmer_frequencies_original.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 ###
###########################################################################
#---------------------------------------------------------------------------------------------------------------------------
#Deal with passed parameters
#---------------------------------------------------------------------------------------------------------------------------
if ($#ARGV == -1) {
usage();
exit;
}
$fasta_file = $ARGV[0];
#$prefix = "Ta";
$k = $ARGV[1];
$prefix = $ARGV[2];
$out_file = "${prefix}_kmers.txt";
unless ( open(IN, "$fasta_file") ) {
print "Got a bad fasta file: $fasta_file\n\n";
exit;
}
unless ( open(OUT, ">$out_file") ) {
print "Couldn't create $out_file\n";
exit;
}
print "Parameters:\nfasta file = $fasta_file\noutput file = $out_file\nk = $k\n";
#---------------------------------------------------------------------------------------------------------------------------
#The main event
#---------------------------------------------------------------------------------------------------------------------------
$start = time();
$seq = "";
$pc = 0;
$linecount = 0;
while (<IN>) {
chomp;
if (/^>/) {
#finish up previous line.
if (length($seq) > 0) {
&process_it;
}
#start new line.
$id = $_;
$id =~ s/^>//g;
$pc++;
if ($pc % 100 == 0) {
print "count = $pc\n";
}
}
else {
$seq = $seq . uc($_);
}
$linecount++;
if ($linecount % 10000 == 0) {
print "line count = $linecount\n";
}
}
#finish up last line.
&process_it;
print "Sorting...\n";
%kmers;
%records;
for $i (sort keys %knucs) {
@parts = split(/\t/, $i);
$record = $parts[0];
$kmer = $parts[1];
if ($kmers{$kmer}) {
$kmers{$kmer} = $kmers{$kmer} + 1;
}
else {
$kmers{$kmer} = 1;
}
if ($records{$record}) {
$records{$record} = $records{$record} + 1;
}
else {
$records{$record} = 1;
}
}
print "Printing...\n";
print OUT "${k}-mer";
for $j (sort keys %records) {
print OUT "\t$prefix_$j";
}
print OUT "\n";
$testsum = 0;
for $i (sort keys %kmers) {
print OUT "$i";
for $j (sort keys %records) {
$key = $j . "\t" . $i;
if ($knucs{$key}) {
print OUT "\t$knucs{$key}";
$testsum = $testsum + $knucs{$key};
}
else {
print OUT "\t0";
}
}
print OUT "\n";
}
#print "TEST SUM = $testsum\n";
close(IN);
close(OUT);
$stop = time();
$total_time = $stop - $start;
print "Total time to run = $total_time\n";
sub usage {
print "Get kmer Frequencies\n";
print "Usage: get_kmer_frequencies.pl <fasta file>\n";
print "This program takes a fasta file, k and prefix as it's parameters.\n\n";
print "It returns a tab delimited file (knucs_out.txt) of kmer counts. (columns = records, rows = kmer counts.)\n\n";
print "Jennifer Meneghin\n";
print "May 11, 2015\n\n";
print "Updated. Now results are returned with summed reverse compliments\n";
print "Jennifer Meneghin\n";
print "February 10, 2016\n\n";
}
sub process_it {
@letters = split(//, $seq);
$end = $#letters - $k + 1;
for $i (0..$end) {
$thiskmer = "";
for $j ($i..($i+$k-1)) {
$thiskmer = $thiskmer . $letters[$j];
}
$rckmer = &rc_seq($thiskmer);
#print "$id\tthiskmer = $thiskmer\n";
#print "$id\trc kmer = $rckmer\n";
if ($thiskmer le $rckmer) {
$key = $id . "\t" . $thiskmer;
}
else { #count goes in rckmer bin instead
$key = $id . "\t" . $rckmer;
}
if ($knucs{$key}) {
$knucs{$key} = $knucs{$key} + 1;
}
else {
$knucs{$key} = 1;
}
}
$seq = "";
$id = "";
}
sub rc_seq {
my ($mykmer) = @_;
my @myletters = split(//,$mykmer);
my (@rcmykmer);
for $i (0..$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 = "";
for $i (0..$k-1) {
$thisrcmykmer = $thisrcmykmer . $rcmykmer[$i];
}
return $thisrcmykmer;
}