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simulate_recombinant_tetrad.pl
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#!/usr/bin/perl
use warnings FATAL => 'all';
use strict;
use Getopt::Long;
use Math::Random qw(:all);
use Math::Round;
use List::Util qw(shuffle);
use Data::Dumper;
##############################################################
# script: simulate_recombinant_tetrad.pl
# author: Jia-Xing Yue (GitHub ID: yjx1217)
# last edited: 2020.01.19
# description: simulating tetrad genotype after meiotic recombination based on input reference genome and marker table
# example: perl simulate_recombinant_tetrad.pl -g ref.genome.raw.relabel.fa(.gz) -g1 S288C -g2 SK1 -m S288C-SK1.ref.final.SNP.markers.txt(.gz) -co_num 90 -nco_num 60 -gc_by_co_ratio 1 -co_gc_size_mean 2500 -co_gc_size_stdev 2000 -nco_gc_size_mean 2200 -nco_gc_size_stdev 2200 -d 10000 -l linked_regions.forSim.txt -m 0 -p Sim
##############################################################
################
# input parameters
################
my $coordinate_genome; # The input genome file for set up the coordinate system (FASTA format)
my $parent1_tag = "P1"; # The genome tag for simulated parent1 genome (P1). Default = "P1".
my $parent2_tag = "P2"; # The genome tag for simulated parent2 genome (P2). Default = "P2".
my $marker_table_file; # SNP markers based on the input genome.
my $co_num = 90; # The number of crossover (CO) per tetrad. Default = 90. # (mean = 90.5 for S. cerevisiae based on Mancera et al. 2008 Nature paper).
my $nco_num = 60; # The number of noncrossover (NCO) per tetrad. Default = 60. # (mean = 66.1 for S. cerevisiae based on Mancera et al. 2008 Nature paper).
my $min_interevent_distance = 10000; # The minimal genomic distance in basepairs (bp) allowed between two independent recombination events. Default = 10000. (i.e. 10 kb).
my $linked_region_bed; # genomic regions for complete linkeage (i.e. no recombination) in 3-column BED format (without header).
my $gc_by_co_ratio = 1; # the ratio of the number of crossover with associated gene conversions (GC) among all crossover events.
my $co_gc_size_mean = 2500; # The mean of crossover-associated gene conversion (CO-GC) size in basepairs (bp). Default = 2500. ("2461.836" for S. cerevisiae based on Mancera et al. 2008 Nature paper).
my $co_gc_size_stdev = 2000; # The standard deviation of crossover-associated gene conversion (CO-GC) size in basepair (bp). Default = 2000. ("2057.673" for S. cerevisiae based on Mancera et al. 2008 Nature paper).
my $nco_gc_size_mean = 2250; # The mean of noncrossover-associated gene conversion (NCO-GC) size in basepairs (bp). Default = 2250. ("2247.716" for NCO-GC for S. cerevisiae based on Mancera et al. 2008 Nature paper).
my $nco_gc_size_stdev=2200; # The standard deviation of noncrossover-associated gene conversion (NCO-GC) size in basepair (bp). Default = 2200. ("2173.46" for NCO-GC for S. cerevisiae based on Mancera et al. 2008 Nature paper).
my $min_gc_size=100; # Safe lower bound gene conversion (GC) size in basepair (bp). Default = 100.
my $max_gc_size=5000; # Safe upper bound gene conversion (GC) size in basepair (bp). Default = 5000.
my $output_prefix = "simulated_tetrad"; # prefix for outputs
my $random_seed = "simulated_tetrad"; # random seed phrase
my $mut_num = 0; # mutation number per tetrad
GetOptions('cg|coordinate_genome_fasta:s' => \$coordinate_genome,
'p1|parent1_tag:s' => \$parent1_tag,
'p2|parent2_tag:s' => \$parent2_tag,
'm|markers:s' => \$marker_table_file,
'co|co_num:i' => \$co_num,
'nco|nco_num:i' => \$nco_num,
'gc_by_co_ratio|gc_by_co_ratio:f' => \$gc_by_co_ratio,
'co_gc_size_mean|co_gc_size_mean:f' => \$co_gc_size_mean,
'co_gc_size_stdev|co_gc_size_stdev:f' => \$co_gc_size_stdev,
'nco_gc_size_mean|nco_gc_size_mean:f' => \$nco_gc_size_mean,
'nco_gc_size_stdev|nco_gc_size_stdev:f' => \$nco_gc_size_stdev,
'min_gc_size|min_gc_size:f' => \$min_gc_size,
'max_gc_size|max_gc_size:f' => \$max_gc_size,
'd|min_interevent_distance:i' => \$min_interevent_distance,
'l|linked_region_bed:s' => \$linked_region_bed,
'mut_num|mut_num:i' => \$mut_num,
'p|prefix:s' => \$output_prefix,
's|seed:s' => \$random_seed);
# initialize the seed for random number generator
random_set_seed_from_phrase($random_seed);
print "\nThis simulation use the random seed: $random_seed\n\n";
my $coordinate_genome_fh = read_file($coordinate_genome);
my %coordinate_genome = ();
my @coordinate_genome = ();
parse_fasta_file($coordinate_genome_fh, \%coordinate_genome, \@coordinate_genome);
close $coordinate_genome_fh;
my $markers_fh = read_file($marker_table_file);
my %markers = ();
parse_markers_table_file($markers_fh, \%markers);
close $markers_fh;
# reconstruct the genome of the two parents based on SNP markers
my %parent1_genome = %coordinate_genome;
my %parent2_genome = %coordinate_genome;
modify_genome_based_on_markers(\%coordinate_genome, \%parent1_genome, \%parent2_genome, \%markers);
my $tetrad_id = "simulated_tetrad";
my @spores = qw(a b c d);
my %initial_genotype_pattern = (
'a' => $parent1_tag,
'b' => $parent1_tag,
'c' => $parent2_tag,
'd' => $parent2_tag,
);
my %spore_id2index = (
'a' => 0,
'b' => 1,
'c' => 2,
'd' => 3,
);
my %spore_index2id = (
0 => 'a',
1 => 'b',
2 => 'c',
3 => 'd',
);
my @initial_genotype_pattern = ($initial_genotype_pattern{'a'}, $initial_genotype_pattern{'b'}, $initial_genotype_pattern{'c'}, $initial_genotype_pattern{'d'});
# create genome space
my %coordinate_genome_space = create_genome_space(\%coordinate_genome);
my $total_coordinate_genome_size = 0;
foreach my $chr (@coordinate_genome) {
if ($coordinate_genome_space{$chr}{'end'} > $total_coordinate_genome_size) {
$total_coordinate_genome_size = $coordinate_genome_space{$chr}{'end'};
}
}
# get infomration for complete linked regions
my %invalid_recomb_regions = ();
if ($linked_region_bed ne "") {
my $linked_region_bed_fh = read_file($linked_region_bed);
parse_linked_regions_file($linked_region_bed_fh, \%invalid_recomb_regions, \%coordinate_genome_space);
}
# simulate recombination
my %recomb_history = ();
my %recomb_breakpoints = ();
foreach my $chr (@coordinate_genome) {
my $chr_start = 1;
my $chr_end = length $coordinate_genome{$chr};
$recomb_breakpoints{$chr}{$chr_start}{'note'} = "chr_start";
$recomb_breakpoints{$chr}{$chr_end}{'note'} = "chr_end";
}
# simulate CO
my %CO = ();
# sample genomic regions
for (my $i = 1; $i <= $co_num; $i++) {
my $co_size;
# determine whether to sample GC tract based on the gc_by_co_ratio
if (random_uniform(1, 0, 1) <= $gc_by_co_ratio) {
# having CO-associated GC
my $co_gc_size = $min_gc_size - 1;
while (($co_gc_size < $min_gc_size) or ($co_gc_size > $max_gc_size)) {
$co_gc_size = random_normal(1, $co_gc_size_mean, $co_gc_size_stdev);
# my $co_gc_size = random_gamma(1, $co_gc_size_gamma_rate, $co_gc_size_gamma_shape) * $co_gc_size_scale;
}
$co_gc_size = round($co_gc_size);
$co_size += $co_gc_size;
} else {
# no CO-associated GC
$co_size = 1;
}
my $chr_sampled = sample_chr($total_coordinate_genome_size, \%coordinate_genome_space, \%invalid_recomb_regions);
my ($interval_start_sampled, $interval_end_sampled) = sample_genomic_interval($co_size, $chr_sampled, \%coordinate_genome_space, \%invalid_recomb_regions);
print "CO:$i > sampled interval with size of $co_size: $chr_sampled:$interval_start_sampled-$interval_end_sampled\n";
$CO{$chr_sampled}{$interval_start_sampled}{'end'} = $interval_end_sampled;
my $key = "${chr_sampled}:${interval_start_sampled}-${interval_end_sampled}";
$invalid_recomb_regions{$key}{'chr'} = $chr_sampled;
if (($interval_start_sampled - $min_interevent_distance) > 1) {
$invalid_recomb_regions{$key}{'start'} = $interval_start_sampled - $min_interevent_distance;
} else {
$invalid_recomb_regions{$key}{'start'} = 1;
}
if (($interval_end_sampled + $min_interevent_distance) < (length $coordinate_genome{$chr_sampled})) {
$invalid_recomb_regions{$key}{'end'} = $interval_end_sampled + $min_interevent_distance;
} else {
$invalid_recomb_regions{$key}{'end'} = length $coordinate_genome{$chr_sampled};
}
my $start_in_genome_space = $coordinate_genome_space{$chr_sampled}{'start'} + $invalid_recomb_regions{$key}{'start'} - 1;
my $end_in_genome_space = $coordinate_genome_space{$chr_sampled}{'start'} + $invalid_recomb_regions{$key}{'end'} - 1;
$invalid_recomb_regions{$key}{'start_in_genome_space'} = $start_in_genome_space;
$invalid_recomb_regions{$key}{'end_in_genome_space'} = $end_in_genome_space;
$invalid_recomb_regions{$key}{'note'} = "existing CO";
if ($interval_start_sampled == $interval_end_sampled) {
$recomb_breakpoints{$chr_sampled}{$interval_start_sampled}{'note'} = "CO_interval_start_and_end";
} else {
$recomb_breakpoints{$chr_sampled}{$interval_start_sampled}{'note'} = "CO_interval_start";
$recomb_breakpoints{$chr_sampled}{$interval_end_sampled}{'note'} = "CO_interval_end";
}
}
my %preliminary_linkage_blocks_by_coord = ();
my %preliminary_linkage_blocks_by_id = ();
my $preliminary_block_id = 0;
foreach my $chr (sort keys %recomb_breakpoints) {
my $offset = 1;
foreach my $bp (sort {$a <=> $b} keys %{$recomb_breakpoints{$chr}}) {
if ( $bp == 1) {
next;
} else {
$preliminary_block_id++;
# for simplicity, here we will use closed intervals to represent each linkage blocks (i.e. not including the exact breakpoints)
my $preliminary_block_start = $offset + 1;
my $preliminary_block_end = $bp - 1;
my $preliminary_block_size = $preliminary_block_end - $preliminary_block_start + 1;
if ($offset == 1) {
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'genotype_pattern'} = join ":", @initial_genotype_pattern;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'genotype_pattern'} = join ":", @initial_genotype_pattern;
}
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_id'} = $preliminary_block_id;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_start'} = $preliminary_block_start;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'chr'} = $chr;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_end'} = $preliminary_block_end;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_size'} = $preliminary_block_size;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'interval_start'} = $offset;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'interval_end'} = $bp;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'chr'} = $chr;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'block_start'} = $preliminary_block_start;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'block_end'} = $preliminary_block_end;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'block_size'} = $preliminary_block_size;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'interval_start'} = $offset;
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'interval_end'} = $bp;
if ($offset eq $bp) {
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'interval_type'} = "CO-GC_interval";
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'interval_type'} = "CO-GC_interval";
} else {
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'interval_type'} = "CO_interval";
$preliminary_linkage_blocks_by_id{$preliminary_block_id}{'interval_type'} = "CO_interval";
}
$offset = $bp;
}
}
}
# simulate CO associated GC
my $CO_id = 0;
my $GC_id = 0;
foreach my $chr (sort keys %CO) {
my %genotype_pattern_before_CO = %initial_genotype_pattern;
my @CO_interval_start_sampled = sort {$a <=> $b} keys %{$CO{$chr}};
foreach my $CO_interval_start (@CO_interval_start_sampled) {
my $CO_interval_end = $CO{$chr}{$CO_interval_start}{'end'};
if ($CO_interval_start eq $CO_interval_end) {
# CO with no GC tract
my $preliminary_block_id_after_CO = $preliminary_linkage_blocks_by_coord{$chr}{$CO_interval_start}{'block_id'};
my $preliminary_block_id_before_CO = $preliminary_block_id_after_CO - 1;
my @genotype_pattern_before_CO = split /:/, $preliminary_linkage_blocks_by_id{$preliminary_block_id_before_CO}{'genotype_pattern'};
my %genotype_pattern_before_CO = ();
for(my $i = 0; $i < 4; $i++) {
my $spore = $spores[$i];
$genotype_pattern_before_CO{$spore} = $genotype_pattern_before_CO[$i];
}
# simulate genotype switch
my ($donor_spore) = random_sample_from_array(1, \@spores);
my $donor_spore_index = $spore_id2index{$donor_spore};
print "donor_spore: $donor_spore, donor_spore_index: $donor_spore_index\n";
my $receipent_spore;
my @available_recipient_spores = ();
foreach my $spore (@spores) {
if (($spore ne $donor_spore) and ($genotype_pattern_before_CO{$spore} ne $genotype_pattern_before_CO{$donor_spore})) {
push @available_recipient_spores, $spore;
}
}
my ($recipient_spore) = random_sample_from_array(1, \@available_recipient_spores);
my $recipient_spore_index = $spore_id2index{$recipient_spore};
print "recipient_spore: $recipient_spore, recipient_spore_index: $recipient_spore_index\n";
my @co_affected_spores = qw(0 0 0 0);
$co_affected_spores[$donor_spore_index] = 1;
$co_affected_spores[$recipient_spore_index] = 1;
my $co_affected_spores = join ":", @co_affected_spores;
my %genotype_pattern_after_CO = ();
# switch genotypes for the donor and recipient
my @genotype_pattern_after_CO = @genotype_pattern_before_CO;
($genotype_pattern_after_CO{$donor_spore}, $genotype_pattern_after_CO{$recipient_spore}) = ($genotype_pattern_before_CO{$recipient_spore}, $genotype_pattern_before_CO{$donor_spore});
$genotype_pattern_after_CO[$donor_spore_index] = $genotype_pattern_after_CO{$donor_spore};
$genotype_pattern_after_CO[$recipient_spore_index] = $genotype_pattern_after_CO{$recipient_spore};
$preliminary_linkage_blocks_by_id{$preliminary_block_id_after_CO}{'genotype_pattern'} = join ":", @genotype_pattern_after_CO;
$preliminary_linkage_blocks_by_coord{$chr}{$CO_interval_start}{'genotype_pattern'} = join ":", @genotype_pattern_after_CO;
$CO_id++;
$recomb_history{'CO'}{$CO_id}{'co_affected_spores'} = $co_affected_spores;
$recomb_history{'CO'}{$CO_id}{'recomb_desc'} = "CO,Type1_CO,$co_affected_spores";
$recomb_history{'CO'}{$CO_id}{'chr'} = $chr;
$recomb_history{'CO'}{$CO_id}{'start'} = $CO_interval_start;
$recomb_history{'CO'}{$CO_id}{'end'} = $CO_interval_end;
$recomb_history{'CO'}{$CO_id}{'subtype'} = "Type1_CO";
} else {
# CO with GC tract
print "chr=$chr, CO_interval_start=$CO_interval_start\n";
my $preliminary_block_id_at_CO = $preliminary_linkage_blocks_by_coord{$chr}{$CO_interval_start}{'block_id'};
my $preliminary_block_id_before_CO = $preliminary_block_id_at_CO - 1;
my $preliminary_block_id_after_CO = $preliminary_block_id_at_CO + 1;
print "preliminary_block_id_before_CO=$preliminary_block_id_before_CO\n";
print "preliminary_block_id_at_CO=$preliminary_block_id_at_CO\n";
print "preliminary_block_id_after_CO=$preliminary_block_id_after_CO\n";
my $genotype_pattern_before_CO = $preliminary_linkage_blocks_by_id{$preliminary_block_id_before_CO}{'genotype_pattern'};
my @genotype_pattern_before_CO = split /:/, $genotype_pattern_before_CO;
my %genotype_pattern_before_CO = ();
print "genotype_pattern_before_CO=$genotype_pattern_before_CO\n";
for(my $i = 0; $i < 4; $i++) {
my $spore = $spores[$i];
$genotype_pattern_before_CO{$spore} = $genotype_pattern_before_CO[$i];
}
# simulate genotype switch
my ($donor_spore) = random_sample_from_array(1, \@spores);
print "donor_spore: $donor_spore\n";
my $donor_spore_index = $spore_id2index{$donor_spore};
print "donor_spore: $donor_spore, donor_spore_index: $donor_spore_index\n";
my $receipent_spore;
my @available_recipient_spores = ();
foreach my $spore (@spores) {
if (($spore ne $donor_spore) and ($genotype_pattern_before_CO{$spore} ne $genotype_pattern_before_CO{$donor_spore})) {
push @available_recipient_spores, $spore;
}
}
my ($recipient_spore) = random_sample_from_array(1, \@available_recipient_spores);
my $recipient_spore_index = $spore_id2index{$recipient_spore};
print "recipient_spore: $recipient_spore, recipient_spore_index: $recipient_spore_index\n";
my @co_affected_spores = qw(0 0 0 0);
$co_affected_spores[$donor_spore_index] = 1;
$co_affected_spores[$recipient_spore_index] = 1;
my $co_affected_spores = join ":", @co_affected_spores;
my %genotype_pattern_after_CO = ();
# switch genotypes for the donor and recipient
($genotype_pattern_after_CO{$donor_spore}, $genotype_pattern_after_CO{$recipient_spore}) = ($genotype_pattern_before_CO{$recipient_spore}, $genotype_pattern_before_CO{$donor_spore});
my @genotype_pattern_after_CO = @genotype_pattern_before_CO;
$genotype_pattern_after_CO[$donor_spore_index] = $genotype_pattern_after_CO{$donor_spore};
$genotype_pattern_after_CO[$recipient_spore_index] = $genotype_pattern_after_CO{$recipient_spore};
my $genotype_pattern_after_CO = join ":", @genotype_pattern_after_CO;
print "genotype_pattern_after_CO=$genotype_pattern_after_CO\n";
$preliminary_linkage_blocks_by_id{$preliminary_block_id_after_CO}{'genotype_pattern'} = $genotype_pattern_after_CO;
$preliminary_linkage_blocks_by_coord{$chr}{$CO_interval_end}{'genotype_pattern'} = $genotype_pattern_after_CO;
my @genotype_pattern_at_CO = @genotype_pattern_before_CO;
# flip a coin to decide which genotype to use for the GC tract
if (random_uniform(1, 0, 1) < 0.5) {
$genotype_pattern_at_CO[$donor_spore_index] = $genotype_pattern_before_CO[$recipient_spore_index];
} else {
$genotype_pattern_at_CO[$recipient_spore_index] = $genotype_pattern_before_CO[$donor_spore_index];
}
my $genotype_pattern_at_CO = join ":", @genotype_pattern_at_CO;
print "genotype_pattern_at_CO=$genotype_pattern_at_CO\n";
$preliminary_linkage_blocks_by_id{$preliminary_block_id_at_CO}{'genotype_pattern'} = $genotype_pattern_at_CO;
$preliminary_linkage_blocks_by_coord{$chr}{$CO_interval_start}{'genotype_pattern'} = $genotype_pattern_at_CO;
$CO_id++;
$recomb_history{'CO'}{$CO_id}{'co_affected_spores'} = $co_affected_spores;
$recomb_history{'CO'}{$CO_id}{'gc_affected_spores'} = $co_affected_spores;
$recomb_history{'CO'}{$CO_id}{'recomb_desc'} = "CO,Type2_CO,$co_affected_spores";
$recomb_history{'CO'}{$CO_id}{'chr'} = $chr;
$recomb_history{'CO'}{$CO_id}{'start'} = $CO_interval_start;
$recomb_history{'CO'}{$CO_id}{'end'} = $CO_interval_end;
$recomb_history{'CO'}{$CO_id}{'subtype'} = "Type2_CO";
$GC_id++;
$recomb_history{'GC'}{$GC_id}{'gc_affected_spores'} = $co_affected_spores;
$recomb_history{'GC'}{$GC_id}{'recomb_desc'} = "GC,Type2_GC,$co_affected_spores";
$recomb_history{'GC'}{$GC_id}{'chr'} = $chr;
$recomb_history{'GC'}{$GC_id}{'start'} = $CO_interval_start;
$recomb_history{'GC'}{$GC_id}{'end'} = $CO_interval_end;
$recomb_history{'GC'}{$GC_id}{'subtype'} = "Type2_GC";
}
}
}
# simulate NCO
my %NCO = ();
for (my $i = 1; $i <= $nco_num; $i++) {
my $nco_size = $min_gc_size - 1;
while (($nco_size < $min_gc_size) or ($nco_size > $max_gc_size)) {
$nco_size = random_normal(1, $nco_gc_size_mean, $nco_gc_size_stdev);
# my $nco_size = random_gamma(1, $nco_gc_size_gamma_rate, $nco_gc_size_gamma_shape) * $nco_gc_size_scale;
}
$nco_size = round($nco_size);
my $chr_sampled = sample_chr($total_coordinate_genome_size, \%coordinate_genome_space, \%invalid_recomb_regions);
my ($interval_start_sampled, $interval_end_sampled) = sample_genomic_interval($nco_size, $chr_sampled, \%coordinate_genome_space, \%invalid_recomb_regions);
print "NCO:$i > sampled interval with size of $nco_size: $chr_sampled:$interval_start_sampled-$interval_end_sampled\n";
$NCO{$chr_sampled}{$interval_start_sampled}{'end'} = $interval_end_sampled;
my $key = "${chr_sampled}:${interval_start_sampled}-${interval_end_sampled}";
$invalid_recomb_regions{$key}{'chr'} = $chr_sampled;
$invalid_recomb_regions{$key}{'start'} = $interval_start_sampled - $min_interevent_distance;
$invalid_recomb_regions{$key}{'end'} = $interval_end_sampled + $min_interevent_distance;
my $start_in_genome_space = $coordinate_genome_space{$chr_sampled}{'start'} + $invalid_recomb_regions{$key}{'start'} - 1;
my $end_in_genome_space = $coordinate_genome_space{$chr_sampled}{'start'} + $invalid_recomb_regions{$key}{'end'} - 1;
$invalid_recomb_regions{$key}{'start_in_genome_space'} = $start_in_genome_space;
$invalid_recomb_regions{$key}{'end_in_genome_space'} = $end_in_genome_space;
$invalid_recomb_regions{$key}{'note'} = "existing NCO";
$recomb_breakpoints{$chr_sampled}{$interval_start_sampled}{'note'} = "NCO_interval_start";
$recomb_breakpoints{$chr_sampled}{$interval_end_sampled}{'note'} = "NCO_interval_end";
}
my $NCO_subblock_id = 0;
my %NCO_interval_end2CO_master_interval_map = ();
foreach my $chr (sort keys %NCO) {
foreach my $NCO_interval_start (sort {$a <=> $b} keys %{$NCO{$chr}}) {
my $NCO_interval_end = $NCO{$chr}{$NCO_interval_start}{'end'};
my $NCO_block_start = $NCO_interval_start + 1;
my $NCO_block_end = $NCO_interval_end - 1;
my $NCO_block_size = $NCO_interval_end - $NCO_block_start + 1;
foreach my $offset (sort {$a <=> $b} keys %{$preliminary_linkage_blocks_by_coord{$chr}}) {
if ($preliminary_linkage_blocks_by_coord{$chr}{$offset}{'interval_type'} eq "CO_interval") {
my $preliminary_block_start = $preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_start'};
my $preliminary_block_end = $preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_end'};
my $genotype_pattern = $preliminary_linkage_blocks_by_coord{$chr}{$offset}{'genotype_pattern'};
if ((($preliminary_block_start <= $NCO_block_start) and ($preliminary_block_end >= $NCO_block_start)) and (($preliminary_block_start <= $NCO_block_end) and ($preliminary_block_end >= $NCO_block_end))) {
my $preliminary_block_id = $preliminary_linkage_blocks_by_coord{$chr}{$offset}{'block_id'};
$NCO_subblock_id++;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'block_id'} = $NCO_subblock_id;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'block_start'} = $NCO_block_start;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'block_end'} = $NCO_block_end;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'interval_start'} = $NCO_interval_start;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'interval_end'} = $NCO_interval_end;
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'interval_type'} = "NCO_interval";
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'block_id'} = "$preliminary_block_id.$NCO_subblock_id";
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'block_start'} = $NCO_block_start;
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'block_end'} = $NCO_block_end;
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'interval_start'} = $NCO_interval_start;
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'interval_end'} = $NCO_interval_end;
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'interval_type'} = "NCO_interval";
$NCO_interval_end2CO_master_interval_map{$chr}{$NCO_interval_end}{'CO_masterblock'}{'block_id'} = $preliminary_block_id;
$NCO_interval_end2CO_master_interval_map{$chr}{$NCO_interval_end}{'CO_masterblock'}{'interval_start'} = $offset;
$NCO_interval_end2CO_master_interval_map{$chr}{$NCO_interval_end}{'CO_masterblock'}{'interval_end'} = $preliminary_linkage_blocks_by_coord{$chr}{$offset}{'interval_end'};
$NCO_interval_end2CO_master_interval_map{$chr}{$NCO_interval_end}{'CO_masterblock'}{'genotype_pattern'} = $genotype_pattern;
my @genotype_pattern_before_NCO = split /:/, $genotype_pattern;
my %genotype_pattern_before_NCO = ();
my %genotype_pattern_at_NCO = ();
my @genotype_pattern_at_NCO = @genotype_pattern_before_NCO;
for(my $i = 0; $i < 4; $i++) {
my $spore = $spores[$i];
$genotype_pattern_at_NCO{$spore} = $genotype_pattern_before_NCO[$i];
}
# simulate genotype switch
my ($donor_spore) = random_sample_from_array(1, \@spores);
my $donor_spore_index = $spore_id2index{$donor_spore};
print "donor_spore: $donor_spore, donor_spore_index: $donor_spore_index\n";
my $receipent_spore;
my @available_recipient_spores = ();
foreach my $spore (@spores) {
if (($spore ne $donor_spore) and ($genotype_pattern_at_NCO{$spore} ne $genotype_pattern_at_NCO{$donor_spore})) {
push @available_recipient_spores, $spore;
}
}
my ($recipient_spore) = random_sample_from_array(1, \@available_recipient_spores);
my $recipient_spore_index = $spore_id2index{$recipient_spore};
print "recipient_spore: $recipient_spore, recipient_spore_index: $recipient_spore_index\n";
my @gc_affected_spores = qw(0 0 0 0);
$gc_affected_spores[$recipient_spore_index] = 1;
my $gc_affected_spores = join ":", @gc_affected_spores;
# switch genotypes for the donor and recipient
$genotype_pattern_at_NCO{$recipient_spore} = $genotype_pattern_at_NCO{$donor_spore};
$genotype_pattern_at_NCO[$recipient_spore_index] = $genotype_pattern_at_NCO{$donor_spore};
$preliminary_linkage_blocks_by_coord{$chr}{$offset}{'NCO_subblock'}{$NCO_subblock_id}{'genotype_pattern'} = join ":", @genotype_pattern_at_NCO;
$preliminary_linkage_blocks_by_coord{$chr}{$NCO_interval_start}{'genotype_pattern'} = join ":", @genotype_pattern_at_NCO;
$GC_id++;
$recomb_history{'GC'}{$GC_id}{'gc_affected_spores'} = $gc_affected_spores;
$recomb_history{'GC'}{$GC_id}{'recomb_desc'} = "GC,Type1_GC,$gc_affected_spores";
$recomb_history{'GC'}{$GC_id}{'chr'} = $chr;
$recomb_history{'GC'}{$GC_id}{'start'} = $NCO_interval_start;
$recomb_history{'GC'}{$GC_id}{'end'} = $NCO_interval_end;
$recomb_history{'GC'}{$GC_id}{'subtype'} = "Type1_GC";
last;
}
}
}
}
}
# generate final linkage blocks
my $final_linkage_blocks = "$output_prefix.$tetrad_id.linkage_blocks.txt";
my $final_linkage_blocks_fh = write_file($final_linkage_blocks);
print $final_linkage_blocks_fh "tetrad_id\tblock_id\tchr\tpos_start-pos_end\tgenotype_pattern\tsegregation_pattern\n";
my %final_linkage_blocks_by_id = ();
my $final_block_id = 0;
my %tetrad_genomes = ();
foreach my $spore (@spores) {
foreach my $chr (@coordinate_genome) {
$tetrad_genomes{$spore}{$chr} = "";
}
}
foreach my $chr (sort keys %recomb_breakpoints) {
my $offset = 1;
foreach my $bp (sort {$a <=> $b} keys %{$recomb_breakpoints{$chr}}) {
if ($bp == 1) {
next;
} else {
# for simplicity, here we will use closed intervals to represent each linkage blocks (i.e. not including the exact breakpoints)
my $final_block_start = $offset + 1;
my $final_block_end = $bp - 1;
my $final_block_size = $final_block_end - $final_block_start + 1;
$final_block_id++;
$final_linkage_blocks_by_id{$final_block_id}{'chr'} = $chr;
$final_linkage_blocks_by_id{$final_block_id}{'interval_start'} = $offset;
$final_linkage_blocks_by_id{$final_block_id}{'interval_end'} = $bp;
print $final_linkage_blocks_fh "$tetrad_id\t$final_block_id\t$chr\t$offset-$bp";
my $parent1_genome_seq = substr $parent1_genome{$chr}, $final_block_start - 1, $final_block_size;
my $parent2_genome_seq = substr $parent2_genome{$chr}, $final_block_start - 1, $final_block_size;
my @genotype_pattern = ();
my $genotype_pattern = "";
my %genotype_pattern = ();
my %segregation_pattern = ();
my @segregation_pattern = (0, 0, 0);
my $segregation_pattern = "";
# print "genome1_seq=$parent1_genome_seq, genome2_seq=$parent2_genome_seq\n";
if ($offset == 1) {
print "breakpoint: chr=$chr, offset=$offset\n";
%genotype_pattern = %initial_genotype_pattern;
@genotype_pattern = @initial_genotype_pattern;
$genotype_pattern = join ":", @genotype_pattern;
@segregation_pattern = (2, 2, 0);
$segregation_pattern = join ":", @segregation_pattern;
print $final_linkage_blocks_fh "\t$genotype_pattern\t$segregation_pattern\n";
$final_linkage_blocks_by_id{$final_block_id}{'genotype_pattern'} = $genotype_pattern;
$final_linkage_blocks_by_id{$final_block_id}{'segregation_pattern'} = $segregation_pattern;
} elsif ($recomb_breakpoints{$chr}{$offset}{'note'} =~ /^(CO_interval_start_and_end|CO_interval_start|CO_interval_end|NCO_interval_start)/) {
print "breakpoint: chr=$chr, offset=$offset\n";
print "breakpoint note: $recomb_breakpoints{$chr}{$offset}{'note'}\n";
$final_linkage_blocks_by_id{$final_block_id}{'genotype_pattern'} = $preliminary_linkage_blocks_by_coord{$chr}{$offset}{'genotype_pattern'};
@genotype_pattern = split ":", $final_linkage_blocks_by_id{$final_block_id}{'genotype_pattern'};
$genotype_pattern = $final_linkage_blocks_by_id{$final_block_id}{'genotype_pattern'};
for (my $i = 0; $i < 4; $i++) {
my $spore = $spores[$i];
my $genotype = $genotype_pattern[$i];
$genotype_pattern{$spore} = $genotype;
}
foreach my $genotype (@genotype_pattern) {
if ($genotype eq $parent1_tag) {
$segregation_pattern[0]++;
} elsif ($genotype eq $parent2_tag) {
$segregation_pattern[1]++;
} elsif ($genotype eq "NA") {
$segregation_pattern[2]++;
} else {
die "unexpected spore genotype: $genotype for the linkage block: $chr:$final_block_start-$final_block_end\n";
}
}
$segregation_pattern = join ":", @segregation_pattern;
print $final_linkage_blocks_fh "\t$genotype_pattern\t$segregation_pattern\n";
$final_linkage_blocks_by_id{$final_block_id}{'genotype_pattern'} = $genotype_pattern;
$final_linkage_blocks_by_id{$final_block_id}{'segregation_pattern'} = $segregation_pattern;
} elsif ($recomb_breakpoints{$chr}{$offset}{'note'} =~ /NCO_interval_end/) {
# NCO end
print "breakpoint: chr=$chr, offset=$offset\n";
print "breakpoint note: $recomb_breakpoints{$chr}{$offset}{'note'}\n";
$genotype_pattern = $NCO_interval_end2CO_master_interval_map{$chr}{$offset}{'CO_masterblock'}{'genotype_pattern'};
@genotype_pattern = split /:/, $genotype_pattern;
for (my $i = 0; $i < 4; $i++) {
my $spore = $spores[$i];
my $genotype = $genotype_pattern[$i];
$genotype_pattern{$spore} = $genotype;
}
foreach my $genotype (@genotype_pattern) {
if ($genotype eq $parent1_tag) {
$segregation_pattern[0]++;
} elsif ($genotype eq $parent2_tag) {
$segregation_pattern[1]++;
} elsif ($genotype eq "NA") {
$segregation_pattern[2]++;
} else {
die "unexpected spore genotype: $genotype for the linkage block: $chr:$final_block_start-$final_block_end\n";
}
}
$segregation_pattern = join ":", @segregation_pattern;
print $final_linkage_blocks_fh "\t$genotype_pattern\t$segregation_pattern\n";
$final_linkage_blocks_by_id{$final_block_id}{'genotype_pattern'} = $genotype_pattern;
$final_linkage_blocks_by_id{$final_block_id}{'segregation_pattern'} = $segregation_pattern;
} else {
print "breakpoint: chr=$chr, offset=$offset\n";
print "breakpoint note: $recomb_breakpoints{$chr}{$offset}{'note'}\n";
die "unexpected breakpoints!!!\n";
}
print "tetrad genome interval: $chr:[$offset - $bp)\n";
foreach my $spore (@spores) {
print "spore=$spore, genotype_pattern=$genotype_pattern{$spore}\n";
my $spore_block_seq = "";
if ($genotype_pattern{$spore} eq "$parent1_tag") {
$spore_block_seq = substr $parent1_genome{$chr}, $offset - 1, $bp - $offset;
} else {
$spore_block_seq = substr $parent2_genome{$chr}, $offset - 1, $bp - $offset;
}
if (exists $tetrad_genomes{$spore}{$chr}) {
$tetrad_genomes{$spore}{$chr} .= $spore_block_seq;
} else {
$tetrad_genomes{$spore}{$chr} = $spore_block_seq;
}
}
$offset = $bp;
}
}
}
close $final_linkage_blocks_fh;
# generate recombination event log
my $recomb_log = "$output_prefix.$tetrad_id.recombination_events.txt";
my $recomb_log_fh = write_file($recomb_log);
my @recomb_types = qw(CO GC);
print $recomb_log_fh "tetrad_id\tevent_id\tevent_type\tevent_subtype\tchr\traw_start\traw_end\tadjusted_start\tadjusted_end\tadjusted_size\taffected_spores\tnote\n";
my $event_id = 0;
my %recomb_event_by_coord = ();
foreach my $recomb_type (@recomb_types) {
foreach my $i (sort {$a <=> $b} keys %{$recomb_history{$recomb_type}}) {
my $chr = $recomb_history{$recomb_type}{$i}{'chr'};
my $start = $recomb_history{$recomb_type}{$i}{'start'};
my $end = $recomb_history{$recomb_type}{$i}{'end'};
my $adjusted_start = $start;
my $adjusted_end = $end;
if ($recomb_type eq "CO") {
$adjusted_start = ($start + $end)/2;
$adjusted_end = ($start + $end)/2;
}
my $size = $end - $start + 1;
my $adjusted_size = $adjusted_end - $adjusted_start + 1;
my $note = "";
my $recomb_desc = $recomb_history{$recomb_type}{$i}{'recomb_desc'};
my @recomb_desc;
if ($recomb_desc =~ /;/) {
@recomb_desc = split /;/, $recomb_desc;
} else {
@recomb_desc = ($recomb_desc);
}
foreach my $desc (@recomb_desc) {
my ($event_type, $event_subtype, $affected_spores) = split /,/, $desc;
$event_id++;
$recomb_event_by_coord{$chr}{$start}{$event_id} = "$tetrad_id\t$event_id\t$event_type\t$event_subtype\t$chr\t$start\t$end\t$adjusted_start\t$adjusted_end\t$adjusted_size\t$affected_spores\t$note";
}
}
}
foreach my $chr (sort keys %recomb_event_by_coord) {
foreach my $start (sort {$a <=> $b} keys %{$recomb_event_by_coord{$chr}}) {
foreach my $event_id (sort {$a <=> $b} keys %{$recomb_event_by_coord{$chr}{$start}}) {
print $recomb_log_fh "$recomb_event_by_coord{$chr}{$start}{$event_id}\n";
}
}
}
close $recomb_log_fh;
my %mutations = ();
if ($mut_num > 0) {
# overlay point mutations
# generate mutation log
my $mut_log = "$output_prefix.$tetrad_id.mutation_events.txt";
my $mut_log_fh = write_file($mut_log);
my %mut_history = ();
my $mut_type = "SNP";
print $mut_log_fh "mutation_type\tmutation_id\tchr\tstart\tend\tsize\taffected_spores\tmutation_description\n";
foreach (my $i = 1; $i <= $mut_num; $i++) {
my %tmp = (); # place_holder for %invalid_recomb_regions
my $chr_sampled = sample_chr($total_coordinate_genome_size, \%coordinate_genome_space, \%tmp);
my $mut_size = 1;
my ($interval_start_sampled, $interval_end_sampled) = sample_genomic_interval($mut_size, $chr_sampled, \%coordinate_genome_space, \%tmp);
print "$mut_type:$i > sampled interval with size of $mut_size: $chr_sampled:$interval_start_sampled-$interval_end_sampled\n";
process_mutation($mut_type, $i, $chr_sampled, $interval_start_sampled, $interval_end_sampled, \%tetrad_genomes, \%mut_history);
}
foreach my $i (sort {$a <=> $b} keys %{$mut_history{$mut_type}}) {
my $chr = $mut_history{$mut_type}{$i}{'chr'};
my $start = $mut_history{$mut_type}{$i}{'start'};
my $end = $mut_history{$mut_type}{$i}{'end'};
my $affected_spores = $mut_history{$mut_type}{$i}{'affected_spores'};
my $size = $end - $start + 1;
my $mut_desc = $mut_history{$mut_type}{$i}{'mut_desc'};
$mutations{$chr}{$start}{'affected_spores'} = $affected_spores;
$mutations{$chr}{$start}{'mut_desc'} = $mut_desc;
print $mut_log_fh "$mut_type\t$i\t$chr\t$start\t$end\t$size\t$affected_spores\t$mut_desc\n";
}
close $mut_log_fh;
}
# output simulated parental genomes
my $parent1_genome_out = "$parent1_tag.genome.fa";
my $parent1_genome_out_fh = write_file($parent1_genome_out);
foreach my $chr (@coordinate_genome) {
print $parent1_genome_out_fh ">$chr\n$parent1_genome{$chr}\n";
}
close $parent1_genome_out_fh;
my $parent2_genome_out = "$parent2_tag.genome.fa";
my $parent2_genome_out_fh = write_file($parent2_genome_out);
foreach my $chr (@coordinate_genome) {
print $parent2_genome_out_fh ">$chr\n$parent2_genome{$chr}\n";
}
close $parent2_genome_out_fh;
# output recombined (and mutated) gamete genomes
foreach my $spore (@spores) {
my $output_spore_genome = "$output_prefix.$tetrad_id.${spore}.genome.fa";
my $output_spore_genome_fh = write_file($output_spore_genome);
foreach my $chr (@coordinate_genome) {
print $output_spore_genome_fh ">$chr\n$tetrad_genomes{$spore}{$chr}\n";
}
close $output_spore_genome_fh;
}
# generate tetrad genotype txt files across all marker sites
my $tetrad_genotype_txt = "$output_prefix.$tetrad_id.genotype.txt";
my $tetrad_genotype_txt_fh = write_file($tetrad_genotype_txt);
foreach my $chr (@coordinate_genome) {
if (exists $markers{$chr}) {
my @markers_chr_pos = sort {$a <=> $b} keys %{$markers{$chr}};
foreach my $i (@markers_chr_pos) {
my $parent1_allele = substr $parent1_genome{$chr}, $i - 1, 1;
my $parent2_allele = $markers{$chr}{$i}{'query_allele'};
# print "chr=$chr i=$i coordinate_genome=$coordinate_genome\n";
print $tetrad_genotype_txt_fh "$chr\t$i\t$coordinate_genome";
my @genotype_pattern = ();
my @segregation_pattern = qw(0 0 0);
foreach my $spore (@spores) {
my $spore_allele = substr $tetrad_genomes{$spore}{$chr}, $i - 1, 1;
if (($spore_allele eq $parent1_allele) and ($parent1_allele ne "NA")) {
push @genotype_pattern, $parent1_tag;
$segregation_pattern[0]++;
} elsif (($spore_allele eq $parent2_allele) and ($parent2_allele ne "NA")) {
push @genotype_pattern, $parent2_tag;
$segregation_pattern[1]++;
} else {
push @genotype_pattern, "NA";
$segregation_pattern[2]++;
}
}
my $genotype_pattern = join "\t", @genotype_pattern;
my $segregation_pattern = join ":", @segregation_pattern;
# my @segregation_pattern_sorted = sort {$b <=> $a} @segregation_pattern;
# my $segregation_pattern_sorted = join ":", @segregation_pattern_sorted;
print $tetrad_genotype_txt_fh "\t$genotype_pattern\n";
}
}
}
close $tetrad_genotype_txt_fh;
my $tetrad_genotype_input_fh = read_file($tetrad_genotype_txt);
my %genotypes = parse_genotype_file($tetrad_genotype_input_fh);
close $tetrad_genotype_input_fh;
my $tetrad_genotype_for_plotting_txt = "$output_prefix.$tetrad_id.genotype.for_genotype_plotting.txt";
my $tetrad_genotype_for_plotting_txt_fh = write_file($tetrad_genotype_for_plotting_txt);
print $tetrad_genotype_for_plotting_txt_fh "chr\tmarker_id\traw_marker_start\traw_marker_end\tadjusted_marker_start\tadjusted_marker_end\tspore_genotype\tspore_id\n";
foreach my $chr (sort keys %genotypes) {
my @pos = sort {$a <=> $b} keys %{$genotypes{$chr}};
my $first_marker_pos = $pos[0];
my $last_marker_pos = $pos[-1];
foreach my $spore_id (@spores) {
my $marker_id = 1;
for (my $i = 0; $i < scalar @pos; $i++) {
my $raw_marker_start = $pos[$i];
my $raw_marker_end = $pos[$i];
my $adjusted_marker_start;
my $adjusted_marker_end;
my $marker_genotype;
if ($pos[$i] == $first_marker_pos) {
$adjusted_marker_start = $pos[$i];
$adjusted_marker_end = ($pos[$i] + $pos[$i+1])/2;
} elsif ($pos[$i] == $last_marker_pos) {
$adjusted_marker_start = ($pos[$i-1] + $pos[$i])/2;
$adjusted_marker_end = $pos[$i];
} else {
$adjusted_marker_start = ($pos[$i-1] + $pos[$i])/2;
$adjusted_marker_end = ($pos[$i] + $pos[$i+1])/2;
}
$marker_genotype = $genotypes{$chr}{$pos[$i]}{$spore_id};
print $tetrad_genotype_for_plotting_txt_fh "$chr\t$marker_id\t$raw_marker_start\t$raw_marker_end\t$adjusted_marker_start\t$adjusted_marker_end\t$marker_genotype\t$spore_id\n";
$marker_id++;
}
}
}
close $tetrad_genotype_for_plotting_txt_fh;
###############
# subroutines (functions)
###############
sub read_file {
my $file = shift @_;
my $fh;
if ($file =~ /\.gz$/) {
open($fh, "gunzip -c $file |") or die "can't open pipe to $file";
} else {
open($fh, $file) or die "can't open $file";
}
return $fh;
}
sub write_file {
my $file = shift @_;
my $fh;
if ($file =~ /\.gz$/) {
open($fh, "| gzip -c >$file") or die "can't open $file\n";
} else {
open($fh, ">$file") or die "can't open $file\n";
}
return $fh;
}
sub parse_fasta_file {
my ($fh, $input_hashref, $input_arrayref) = @_;
my $seq_name = "";
while (<$fh>) {
chomp;
if (/^\s*$/) {
next;
} elsif (/^\s*#/) {
next;
} elsif (/^>(.*)/) {
$seq_name = $1;
push @$input_arrayref, $seq_name;
$$input_hashref{$seq_name} = "";
} else {
$$input_hashref{$seq_name} .= $_;
}
}
}
sub parse_markers_table_file {
my ($fh, $markers_hashref) = @_;
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
/^chr\tstart\tend/ and next;
/^ref_chr\tref_start\tref_end/ and next;
/^parent1_chr\tparent1_start\tparent1_end/ and next;
/^parent2_chr\tparent2_start\tparent2_end/ and next;
my ($ref_chr, $ref_start, $ref_end, $ref_allele, $query_allele, $query_chr, $query_start, $query_end, $match_orientation) = split /\t/, $_;
$$markers_hashref{$ref_chr}{$ref_start}{'ref_chr'} = $ref_chr;
$$markers_hashref{$ref_chr}{$ref_start}{'ref_start'} = $ref_start;
$$markers_hashref{$ref_chr}{$ref_start}{'ref_end'} = $ref_end;
$$markers_hashref{$ref_chr}{$ref_start}{'ref_allele'} = $ref_allele;
$$markers_hashref{$ref_chr}{$ref_start}{'query_chr'} = $query_chr;
$$markers_hashref{$ref_chr}{$ref_start}{'query_start'} = $query_start;
$$markers_hashref{$ref_chr}{$ref_start}{'query_end'} = $query_end;
$$markers_hashref{$ref_chr}{$ref_start}{'query_allele'} = $query_allele;
$$markers_hashref{$ref_chr}{$ref_start}{'match_orientation'} = $match_orientation;
}
}
sub modify_genome_based_on_markers {
my ($genome_hashref, $parent1_genome_hashref, $parent2_genome_hashref, $markers_hashref) = @_;
my $count = 0;
foreach my $chr (sort keys %$genome_hashref) {
foreach my $pos (sort {$a <=> $b} keys %{$$markers_hashref{$chr}}) {
substr $$parent1_genome_hashref{$chr}, $pos - 1, 1, $$markers_hashref{$chr}{$pos}{'ref_allele'};
substr $$parent2_genome_hashref{$chr}, $pos - 1, 1, $$markers_hashref{$chr}{$pos}{'query_allele'};
$count++;
}
}
print "reconstruct genome1 and genome2 by replace $count markers in the input genome\n";
}
# create genome space
sub create_genome_space {
my $genome_hashref = shift @_;
my %genome_space = ();
my $offset = 0;
foreach my $chr (sort keys %$genome_hashref) {
my $chr_length = length $$genome_hashref{$chr};
my $start = $offset + 1;
my $end = $start + $chr_length - 1;
$genome_space{$chr}{"start"} = $start;
$genome_space{$chr}{"end"} = $end;
$genome_space{$chr}{"size"} = $chr_length;
print "chr=$chr, chr_length=$chr_length, genome_space_start=$start, genome_space_end=$end\n";
$offset = $end;
}
return %genome_space;
}
sub parse_linked_regions_file {
my ($fh, $invalid_recomb_regions_hashref, $genome_space_hashref) = @_;
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
my ($chr, $start, $end) = split /\t/, $_;
my $start_in_genome_space = $$genome_space_hashref{$chr}{'start'} + $start - 1;
my $end_in_genome_space = $$genome_space_hashref{$chr}{'start'} + $end - 1;
my $key = "${chr}:${start}-${end}";
$$invalid_recomb_regions_hashref{$key}{'chr'} = $chr;
$$invalid_recomb_regions_hashref{$key}{'start'} = $start;
$$invalid_recomb_regions_hashref{$key}{'end'} = $end;
$$invalid_recomb_regions_hashref{$key}{'start_in_genome_space'} = $start_in_genome_space;
$$invalid_recomb_regions_hashref{$key}{'end_in_genome_space'} = $end_in_genome_space;
if (($start == 1) and ($end == ($$genome_space_hashref{$chr}{'end'} - $$genome_space_hashref{$chr}{'start'} + 1))) {
$$invalid_recomb_regions_hashref{$key}{'note'} = "predefined_complete_chr";
print "complete linked chromosome: $chr\n";
} else {
$$invalid_recomb_regions_hashref{$key}{'note'} = "predefined_region";
}
print "invalid recombination region: $chr:$start-$end in genome space: ${start_in_genome_space}-${end_in_genome_space}\n";
}
}
sub genome_space_translator {
my ($raw, $genome_space_hashref) = @_;
my ($chr_translated, $pos_translated);
foreach my $chr (sort keys %$genome_space_hashref) {
my $chr_start = $$genome_space_hashref{$chr}{'start'};
my $chr_end = $$genome_space_hashref{$chr}{'end'};
if (($raw >= $chr_start) and ($raw <= $chr_end)) {
$chr_translated = $chr;
$pos_translated = $raw - $chr_start + 1;
last;
}
}
return ($chr_translated, $pos_translated);
}
sub sample_chr {
my ($total_genome_size, $genome_space_hashref, $invalid_recomb_regions_hashref) = @_;
my $chr_sampling;
SAMPLE:
$chr_sampling = random_uniform(1, 1, $total_genome_size);
print "\nchr_sampling = $chr_sampling\n";
$chr_sampling = round($chr_sampling);
# check for invalid chromosome
foreach my $key (sort keys %$invalid_recomb_regions_hashref) {
if ($$invalid_recomb_regions_hashref{$key}{'note'} eq "predefined_complete_chr") {
my $start_in_genome_space = $$invalid_recomb_regions_hashref{$key}{'start_in_genome_space'};
my $end_in_genome_space = $$invalid_recomb_regions_hashref{$key}{'end_in_genome_space'};
if (($chr_sampling >= $start_in_genome_space) and ($chr_sampling <= $end_in_genome_space)) {
print "overlapped with invalid chromosome: $key, re-do sampling\n";
goto SAMPLE;
}
}
}
my ($chr_sampled, $start_sampled) = genome_space_translator($chr_sampling, $genome_space_hashref);
print "chr_sampled = $chr_sampled\n";
return $chr_sampled;
}
sub sample_genomic_interval {
my ($interval_size, $chr, $genome_space_hashref, $invalid_recomb_regions_hashref) = @_;
my $chr_length = $$genome_space_hashref{$chr}{'size'};
my ($interval_start_sampled, $interval_end_sampled);
SAMPLE:
$interval_start_sampled = random_uniform(1, 1, $chr_length - $interval_size + 1);
$interval_start_sampled = round($interval_start_sampled);
$interval_end_sampled = $interval_start_sampled + $interval_size - 1;
print "initially sampled interval: ${interval_start_sampled}-${interval_end_sampled}\n";
# check for the overlap with invalid regions, if so, re-do sampling
foreach my $key (sort keys %$invalid_recomb_regions_hashref) {
if ($$invalid_recomb_regions_hashref{$key}{'chr'} eq $chr) {
my $invalid_region_start = $$invalid_recomb_regions_hashref{$key}{'start'};
my $invalid_region_end = $$invalid_recomb_regions_hashref{$key}{'end'};
if (($interval_start_sampled <= $invalid_region_start) and ($interval_end_sampled >= $invalid_region_start)) {
print "overlapped with ${invalid_region_start}-${invalid_region_end}, re-do sampling\n";
goto SAMPLE;
} elsif (($interval_end_sampled >= $invalid_region_start) and ($interval_start_sampled <= $invalid_region_end)) {
print "overlapped with ${invalid_region_start}-${invalid_region_end}, re-do sampling\n";
goto SAMPLE;
}
}
}
print "final sampled interval: ${interval_start_sampled}-${interval_end_sampled}\n";
return ($interval_start_sampled, $interval_end_sampled)
}