174 lines
3.2 KiB
Perl
174 lines
3.2 KiB
Perl
package KmerNode;
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use strict;
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use warnings;
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use Carp;
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use ReadTracker;
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use base qw (GenericNode);
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sub new {
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my $packagename = shift;
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my ($kmer_seq, $accession) = @_;
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my $self = $packagename->SUPER::new($kmer_seq);
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$self->{_count} = 0;
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$self->{_ReadTracker} = new ReadTracker();
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$self->{depth} = undef;
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## for DP scans:
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$self->{_visited} = 0;
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$self->{_base_score} = 0;
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$self->{_sum_score} = 0;
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$self->{_best_prev} = undef; # prev_node in highest scoring path.
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$self->{_forward_scores} = []; # stores structs of { node => ref, score => $score}
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bless ($self, $packagename);
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return($self);
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}
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####
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sub get_ReadTracker {
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my $self = shift;
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return($self->{_ReadTracker});
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}
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sub get_sequence {
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my $self = shift;
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return($self->get_value());
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}
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sub set_sequence {
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my $self = shift;
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my $sequence = shift;
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unless ($sequence =~ /\w/) {
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confess "Error, need sequence";
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}
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$self->set_value($sequence);
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return;
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}
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sub track_reads {
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my $self = shift;
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my @accs = @_;
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$self->{_ReadTracker}->track_reads(@accs);
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return;
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}
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sub get_count {
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my $self = shift;
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return($self->{_count});
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}
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sub set_count {
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my $self = shift;
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my ($count) = @_;
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$self->{_count} = $count;
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return;
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}
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####
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sub toString {
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my $self = shift;
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my @prev_nodes = $self->get_all_prev_nodes();
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my @next_nodes = $self->get_all_next_nodes();
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my $text = "";
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foreach my $prev_node (@prev_nodes) {
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$text .= "P " . $prev_node->get_value() . "(" . $prev_node->get_count() . ") $prev_node " . join(",", $prev_node->get_colors()) . "\n";
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}
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$text .= "X " . $self->get_value() . "(" . $self->get_count() . ") $self " . join(",", $self->get_colors()) . "\n";
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foreach my $next_node (@next_nodes) {
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$text .= "N " . $next_node->get_value() . "(" . $self->get_count() . ") $next_node " . join(",", $next_node->get_colors()) . "\n";
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}
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return($text);
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}
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####
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sub get_reads_exiting_node {
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my $self = shift;
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my @next_nodes = $self->get_all_next_nodes();
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unless (@next_nodes) {
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return();
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}
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my $read_tracker = $self->get_ReadTracker();
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my @reads_in_node = $read_tracker->get_tracked_read_indices();
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my @reads_in_next_nodes;
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foreach my $next_node (@next_nodes) {
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push (@reads_in_next_nodes, $next_node->get_ReadTracker()->get_tracked_read_indices());
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}
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my %next_node_reads = map { + $_ => 1 } @reads_in_next_nodes;
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my @exiting_reads;
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foreach my $read (@reads_in_node) {
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if ($next_node_reads{$read}) {
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push (@exiting_reads, $read);
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}
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}
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return(@exiting_reads);
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}
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####
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sub get_reads_entering_node {
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my $self = shift;
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my @prev_nodes = $self->get_all_prev_nodes();
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unless (@prev_nodes) {
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return();
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}
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my $read_tracker = $self->get_ReadTracker();
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my @reads_in_node = $read_tracker->get_tracked_read_indices();
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my @reads_in_prev_nodes;
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foreach my $prev_node (@prev_nodes) {
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push (@reads_in_prev_nodes, $prev_node->get_ReadTracker()->get_tracked_read_indices());
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}
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my %prev_node_reads = map { + $_ => 1 } @reads_in_prev_nodes;
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my @entering_reads;
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foreach my $read (@reads_in_node) {
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if ($prev_node_reads{$read}) {
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push (@entering_reads, $read);
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}
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}
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return(@entering_reads);
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}
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1; #EOM
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