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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
## hexamer stats
my %framed_hexamers;
my %background_hexamers;
## pentamer stats
my %framed_pentamers;
my %background_base_probs;
my %framed_all_pentamer_counts;
my $usage = "usage: $0 targetCDSs base_probs.dat\n\n";
my $target_CDS = $ARGV[0] or die $usage;
my $base_probs_dat_file = $ARGV[1] or die $usage;
my $debug = $ARGV[2];
main: {
&parse_targetCDSs($target_CDS);
&parse_background($base_probs_dat_file);
&add_pseudocounts();
&report_logliklihood_ratios();
exit(0);
}
####
sub report_logliklihood_ratios {
## Markov-based probabilities (5th order markov chain):
foreach my $framed_hexamer (sort keys %framed_hexamers) {
my ($hexamer, $frame) = split (/-/, $framed_hexamer);
if ($hexamer =~ /[^GATC]/) {
## ignoring hexamers containing non-GATC bases
next;
}
my $pentamer = substr($hexamer, 0, 5);
my $framed_hexamer_count = $framed_hexamers{$framed_hexamer};
my $framed_pentamer_count = $framed_pentamers{"${pentamer}-${frame}"};
my $markov_prob_framed = $framed_hexamer_count / $framed_pentamer_count;
my $last_base = substr($hexamer, 5, 1);
my $background_prob = $background_base_probs{$last_base} or die "Error, no background probability set for base: $last_base of hexamer $hexamer";;
my $logliklihood = log($markov_prob_framed / $background_prob);
print "$framed_hexamer\t$logliklihood\n";
}
## The Initialization Matrix based on framed pentamer frequencies.
foreach my $framed_pentamer (sort keys %framed_pentamers) {
if ($framed_pentamer =~ /[^GATC]/) {
next;
}
my ($pentamer, $frame) = split (/-/, $framed_pentamer);
my $frame_counts = $framed_all_pentamer_counts{$frame};
my $framed_pentamer_counts = $framed_pentamers{$framed_pentamer};
my $prob_framed_pentamer = $framed_pentamer_counts / $frame_counts;
## now background
my @bases = split(//, $pentamer);
my $prob_background_pentamer = 1;
foreach my $base (@bases) {
$prob_background_pentamer *= $background_base_probs{$base};
}
my $logliklihood = log($prob_framed_pentamer / $prob_background_pentamer);
print "$framed_pentamer\t$logliklihood\n";
}
return;
}
####
sub add_pseudocounts {
foreach my $framed_hexamer (keys %framed_hexamers) {
my ($hexamer, $frame) = split (/-/, $framed_hexamer);
my $pentamer = substr($hexamer, 0, 5);
$framed_hexamers{$framed_hexamer}++;
$framed_pentamers{"${pentamer}-${frame}"}++;
$framed_all_pentamer_counts{$frame}++;
}
return;
}
####
sub parse_targetCDSs {
my ($seqFile) = @_;
my $fasta_reader = new Fasta_reader($seqFile);
while (my $seq_obj = $fasta_reader->next()) {
my $accession = $seq_obj->get_accession();
print STDERR "\r Target: processing $accession " if $debug;
my $sequence = uc $seq_obj->get_sequence();
my $seq_len = length($sequence);
for (my $i = 0; $i <= $seq_len - 5; $i++) {
my $frame = $i % 3;
my $pentamer = substr($sequence, $i, 5);
$framed_pentamers{"${pentamer}-${frame}"}++;
$framed_all_pentamer_counts{$frame}++;
if ($i <= $seq_len - 6) {
# got a hexamer
my $hexamer = substr($sequence, $i, 6);
$framed_hexamers{"${hexamer}-${frame}"}++;
}
}
}
print "\r CDS base frequency processing complete. \n" if $debug;
return;
}
####
sub parse_background {
my ($base_probs_dat_file) = @_;
open (my $fh, $base_probs_dat_file) or die "Error, cannot open file $base_probs_dat_file";
while (<$fh>) {
chomp;
my ($base, $count, $ratio) = split(/\t/);
$background_base_probs{$base} = $ratio;
}
close $fh;
return;
}
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