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package Simulate::Uniform_Read_Generator;
use strict;
use warnings;
use Carp;
use Data::Dumper;
sub new {
my $packagename = shift;
my $params_struct = shift;
# params should have format:
# {
# coordsets => [ [lend,rend], [lend,rend], ...],
# mean_fragment_length => int,
# fragment_length_stdev => int,
# read_length => int,
# }
unless (ref $params_struct eq "HASH") {
confess "Error, params struct required";
}
my $coordsets_aref = $params_struct->{coordsets} or confess "Error, need coordsets parameter";
my $mean_fragment_length = $params_struct->{mean_fragment_length} or confess "Error, need mean_fragment_length parameter";
my $fragment_length_stdev = $params_struct->{fragment_length_stdev} or confess "Error, need fragment_length_stdev parameter";
my $read_length = $params_struct->{read_length} or confess "Error, need read_length parameter";
my $self = { _coordsets => undef, # note, this is reconfigured below, not the same as the input parameter
mean_fragment_length => $mean_fragment_length,
fragment_length_stdev => $fragment_length_stdev,
read_length => $read_length,
};
bless($self, $packagename);
$self->_init_coordsets($coordsets_aref);
return($self);
}
####
sub _init_coordsets {
my $self = shift;
my ($coordsets_aref) = @_;
my @ordered_coordsets = sort {$a->[0]<=>$b->[0]} @$coordsets_aref;
my @coord_structs;
my $prev_cdna_coord = 0;
foreach my $coordset (@ordered_coordsets) {
my ($lend, $rend) = @$coordset;
my $cdna_lend = $prev_cdna_coord + 1; ## cdna-relative coordinates
my $cdna_rend = $cdna_lend + ($rend - $lend);
my $struct = { lend => $lend,
rend => $rend,
cdna_lend => $cdna_lend,
cdna_rend => $cdna_rend,
};
push (@coord_structs, $struct);
$prev_cdna_coord = $cdna_rend;
}
$self->{_coordsets} = \@coord_structs;
return;
}
####
sub simulate_paired_reads_random_pos {
my $self = shift;
my ($num_reads) = @_;
unless (defined($num_reads) && $num_reads =~ /\d/) {
confess "Error, need num reads to simulate";
}
my $frag_length = $self->{mean_fragment_length};
my $max_cdna_rend = $self->_get_max_cdna_rend();
if ($frag_length > $max_cdna_rend) {
$frag_length = $max_cdna_rend;
}
my @reads; # to contain ( [ left_read_aref, right_read_aref], ... )
for (1..$num_reads) {
my $read_start_pos = int( rand($max_cdna_rend - $frag_length + 1)) + 1; # uniform selection of potential start sites.
# simulate a fragment according to fragment length
my @fragment = $self->_simulate_fragment($read_start_pos);
# sample from each end to generate reads
my @left_read_segs = $self->_get_left_fragment_read(@fragment);
my @right_read_segs = $self->_get_right_fragment_read(@fragment);
push (@reads, [ [@left_read_segs], [@right_read_segs] ] );
## simulate reads from fragment
## always do pairs and let the caller decide on which end or both to leverage.
}
return(@reads);
}
####
sub simulate_paired_reads_uniformly_across_seq {
my $self = shift;
my $frag_length = $self->{mean_fragment_length};
my $max_cdna_rend = $self->_get_max_cdna_rend();
if ($frag_length > $max_cdna_rend) {
$frag_length = $max_cdna_rend;
}
my @reads; # to contain ( [ left_read_aref, right_read_aref], ... )
for my $read_start_pos (1..($max_cdna_rend - $frag_length + 1)) {
# simulate a fragment according to fragment length
my @fragment = $self->_simulate_fragment($read_start_pos);
# sample from each end to generate reads
my @left_read_segs = $self->_get_left_fragment_read(@fragment);
my @right_read_segs = $self->_get_right_fragment_read(@fragment);
push (@reads, [ [@left_read_segs], [@right_read_segs] ] );
## simulate reads from fragment
## always do pairs and let the caller decide on which end or both to leverage.
}
return(@reads);
}
####
sub _simulate_fragment {
my $self = shift;
my ($read_start_pos) = @_;
my $frag_length = $self->{mean_fragment_length};
my $max_cdna_rend = $self->_get_max_cdna_rend();
if ($frag_length > $max_cdna_rend) {
$frag_length = $max_cdna_rend;
}
my @read_coords;
my $structs_aref = $self->{_coordsets};
my $read_cdna_lend_pos = $read_start_pos; #$self->_get_cdna_coord_via_genome_coord($read_start_pos);
my $len_remaining = $frag_length;
foreach my $struct (@$structs_aref) {
my $exon_genome_lend = $struct->{lend};
my $exon_genome_rend = $struct->{rend};
my $exon_cdna_lend = $struct->{cdna_lend};
my $exon_cdna_rend = $struct->{cdna_rend};
if ($exon_cdna_lend <= $read_cdna_lend_pos && $read_cdna_lend_pos <= $exon_cdna_rend) {
## convert read lend position to genome coordinate position.
my $delta = $read_cdna_lend_pos - $exon_cdna_lend;
my $read_genome_lend = $exon_genome_lend + $delta;
my $read_exon_len = $exon_cdna_rend - $read_cdna_lend_pos + 1;
if ($read_exon_len >= $len_remaining) {
my $read_genome_rend = $read_genome_lend + $len_remaining -1;
push (@read_coords, [$read_genome_lend, $read_genome_rend]);
last;
}
else {
my $read_genome_rend = $exon_genome_rend;
my $len_added = $read_genome_rend - $read_genome_lend + 1;
push (@read_coords, [$read_genome_lend, $read_genome_rend]);
$len_remaining -= $len_added;
$read_cdna_lend_pos += $len_added;
}
}
}
return(@read_coords);
}
####
sub _get_max_cdna_rend {
my $self = shift;
my $structs_aref = $self->{_coordsets};
my $max_cdna_rend = $structs_aref->[$#$structs_aref]->{cdna_rend};
return($max_cdna_rend);
}
####
sub _get_cdna_coord_via_genome_coord {
my $self = shift;
my ($cdna_coord) = @_;
my $structs_aref = $self->{_coordsets};
foreach my $struct (@$structs_aref) {
my $exon_genome_lend = $struct->{lend};
my $exon_genome_rend = $struct->{rend};
my $exon_cdna_lend = $struct->{cdna_lend};
my $exon_cdna_rend = $struct->{cdna_rend};
if ($cdna_coord >= $exon_cdna_lend && $cdna_coord <= $exon_cdna_rend) {
my $delta = $cdna_coord - $exon_cdna_lend;
my $genome_coord = $exon_genome_lend += $delta;
return($genome_coord);
}
}
confess "Error, could not map coordinate $cdna_coord within coordsets: " . Dumper($structs_aref);
}
####
sub _get_left_fragment_read {
my $self = shift;
my @frag = @_;
my $read_length = $self->{read_length};
my $length_remaining = $read_length;
my @read_coords;
foreach my $segment (@frag) {
my ($frag_lend, $frag_rend) = @$segment;
my $seg_len = $frag_rend - $frag_lend + 1;
if ($seg_len >= $length_remaining) {
my $read_seg = [$frag_lend, $frag_lend + $length_remaining - 1];
push (@read_coords, $read_seg);
last;
}
else {
push (@read_coords, [$frag_lend, $frag_rend]);
$length_remaining -= $seg_len;
}
}
return(@read_coords);
}
####
sub _get_right_fragment_read {
my $self = shift;
my @frag = @_;
my $read_length = $self->{read_length};
my $length_remaining = $read_length;
my @read_coords;
foreach my $segment (reverse @frag) {
my ($frag_lend, $frag_rend) = @$segment;
my $seg_len = $frag_rend - $frag_lend + 1;
if ($seg_len >= $length_remaining) {
my $read_seg = [$frag_rend - $length_remaining + 1, $frag_rend];
push (@read_coords, $read_seg);
last;
}
else {
push (@read_coords, [$frag_lend, $frag_rend]);
$length_remaining -= $seg_len;
}
}
@read_coords = reverse @read_coords;
return(@read_coords);
}
1; #EOM
|
