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batch_tetrad_genotyping_by_parent_genomes.pl
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#!/usr/bin/perl
use warnings FATAL => 'all';
use strict;
use Getopt::Long;
use Cwd;
# use Data::Dumper;
##############################################################
# script: batch_tetrad_genotying_by_parent_genomes.pl
# author: Jia-Xing Yue (GitHub ID: yjx1217)
# last edited: 2019.09.09
# description: run batch tetrad-based genotyping based on the mpileup files of spores
# example: perl batch_tetrad_genotyping_by_parent_genomes.pl -s Master_Sample_Table.txt -m SNP -c ./../../data/chr_list.yeast.txt -q 30 -marker_dir ./../14.Polymorphic_Markers_by_Consensus -b batch_id -gamete_read_mapping_dir ./../15.Gamete_Read_Mapping_to_Parent_Genomes -output_dir output_dir
##############################################################
my ($sample_table, $marker_type, $chr_list, $basecall_qual_diff_cutoff, $basecall_purity_cutoff, $marker_dir, $batch_id, $gamete_read_mapping_dir, $output_dir, $apply_cnv_filter, $allow_heteroduplex);
$batch_id = "Batch_TEST";
$marker_type = "SNP";
$basecall_qual_diff_cutoff = 30;
$basecall_purity_cutoff = 0.9;
$output_dir = "$batch_id";
$marker_dir = "./../14.Polymorphic_Markers_by_Consensus";
$gamete_read_mapping_dir = "./../15.Gamete_Read_Mapping_to_Parent_Genomes";
$apply_cnv_filter = "no";
$allow_heteroduplex = "no";
GetOptions('sample_table|s:s' => \$sample_table, # master sample list
'marker_type|m:s' => \$marker_type, # SNP or INDEL or BOTH
'qual|q:i' => \$basecall_qual_diff_cutoff, # 30
'purity|p:f' => \$basecall_purity_cutoff, # 30
'chr_list|c:s' => \$chr_list,
'marker_dir|m_dir:s' => \$marker_dir,
'batch_id|b:s' => \$batch_id,
'apply_cnv_filter:s' => \$apply_cnv_filter,
'allow_heteroduplex:s' => \$allow_heteroduplex,
'gamete_read_mapping_dir|orm_dir:s' => \$gamete_read_mapping_dir,
'output_dir|o:s' => \$output_dir);
my $sample_table_fh = read_file($sample_table);
my $chr_list_fh = read_file($chr_list);
my @chr = parse_list_file($chr_list_fh);
my %tetrads = parse_sample_table_by_tetrad($sample_table_fh);
close $sample_table_fh;
my $base_dir = cwd();
system("mkdir $output_dir");
foreach my $tetrad_id (sort keys %tetrads) {
my $cross_pair = $tetrads{$tetrad_id}{'cross_pair'};
my ($genome1_tag, $genome2_tag) = split "-", $cross_pair;
print "tetrad: $tetrad_id, cross_pair: $cross_pair, parent1: $genome1_tag, parent2: $genome2_tag\n";
$marker_type = uc $marker_type;
my %markers = ();
print "get markers ...\n";
get_markers($genome1_tag, $genome2_tag, $marker_dir, $marker_type, \%markers);
my %genotypes = ();
my %mutations = ();
my %heteroduplex = ();
# my @spore_indices = qw(a b c d);
my @spore_indices = @{$tetrads{$tetrad_id}{'spore_index'}};
# raw genotype calling
print "raw genotype calling ...\n";
foreach my $spore_index (@spore_indices) {
my $spore_id = "$tetrad_id.$spore_index";
my $genome1_based_spore_dir = "${gamete_read_mapping_dir}/${batch_id}/${cross_pair}.${spore_id}.${genome1_tag}";
my $genome1_based_spore_mpileup = "${genome1_based_spore_dir}/${cross_pair}.${spore_id}.${genome1_tag}.mpileup.gz";
if (-f $genome1_based_spore_mpileup) {
my $genome1_based_spore_mpileup_fh = read_file($genome1_based_spore_mpileup);
parse_mpileup_file($spore_id, $spore_index, $cross_pair, $genome1_tag, $genome2_tag, $genome1_based_spore_mpileup_fh, $allow_heteroduplex, \%markers, \%genotypes, \%mutations, \%heteroduplex);
if ($apply_cnv_filter eq "yes") {
my $genome1_based_spore_cnv = "${genome1_based_spore_dir}/${cross_pair}.${spore_id}.${genome1_tag}.CNV_significance_test.txt";
my $genome1_based_spore_cnv_fh = read_file($genome1_based_spore_cnv);
filter_genotype_by_cnv($spore_id, $spore_index, $cross_pair, $genome1_tag, $genome2_tag, $genome1_based_spore_cnv_fh, \%genotypes, \%mutations, \%heteroduplex);
}
}
my $genome2_based_spore_dir = "${gamete_read_mapping_dir}/${batch_id}/${cross_pair}.${spore_id}.${genome2_tag}";
my $genome2_based_spore_mpileup = "${genome2_based_spore_dir}/${cross_pair}.${spore_id}.${genome2_tag}.mpileup.gz";
if (-f $genome2_based_spore_mpileup) {
my $genome2_based_spore_mpileup_fh = read_file($genome2_based_spore_mpileup);
parse_mpileup_file($spore_id, $spore_index, $cross_pair, $genome2_tag, $genome1_tag, $genome2_based_spore_mpileup_fh, $allow_heteroduplex, \%markers, \%genotypes, \%mutations, \%heteroduplex);
if ($apply_cnv_filter eq "yes") {
my $genome2_based_spore_cnv = "${genome2_based_spore_dir}/${cross_pair}.${spore_id}.${genome2_tag}.CNV_significance_test.txt";
my $genome2_based_spore_cnv_fh = read_file($genome2_based_spore_cnv);
filter_genotype_by_cnv($spore_id, $spore_index, $cross_pair, $genome2_tag, $genome1_tag, $genome2_based_spore_cnv_fh, \%genotypes, \%mutations, \%heteroduplex);
}
}
}
# cross check between ${genome1_tag}-${genome2_tag}.${genome1_tag} based signals and ${genome1_tag}-${genome2_tag}.${genome2_tag} based signals
crosscheck_genotypes($tetrad_id, $genome1_tag, $genome2_tag, \%markers, \%genotypes);
crosscheck_mutations($tetrad_id, $genome1_tag, $genome2_tag, \%markers, \%mutations);
crosscheck_heteroduplex($tetrad_id, $genome1_tag, $genome2_tag, \%markers, \%heteroduplex);
my $prefix;
# output_by_parent1
print "output genotypes based parent1: $genome1_tag\n";
$prefix = "$base_dir/$output_dir/$cross_pair.$tetrad_id.$genome1_tag.q${basecall_qual_diff_cutoff}";
output_genotypes($prefix, $tetrad_id, $cross_pair, $genome1_tag, $genome2_tag, \@chr, \%genotypes, \%mutations, \%heteroduplex);
# output_by_parent2
print "output genotypes based parent2: $genome2_tag\n";
$prefix = "$base_dir/$output_dir/$cross_pair.$tetrad_id.$genome2_tag.q${basecall_qual_diff_cutoff}";
output_genotypes($prefix, $tetrad_id, $cross_pair, $genome2_tag, $genome1_tag, \@chr, \%genotypes, \%mutations, \%heteroduplex);
}
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_sample_table_by_tetrad {
my $fh = shift @_;
my %sample_table = ();
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
my ($sample_id, $tetrad_id, $spore_id, $PE_reads_files, $cross_pair, $note) = split /\s+/, $_;
if (exists $sample_table{$tetrad_id}{'spore_index'}) {
push @{$sample_table{$tetrad_id}{'spore_index'}}, $spore_id;
} else {
@{$sample_table{$tetrad_id}{'spore_index'}} = ($spore_id);
}
$sample_table{$tetrad_id}{'cross_pair'} = $cross_pair;
$sample_table{$tetrad_id}{'note'} = $note;
}
return %sample_table;
}
sub parse_list_file {
my $fh = shift @_;
my @chr = ();
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
push @chr, $_;
}
return @chr;
}
sub get_markers {
my ($genome1_tag, $genome2_tag, $marker_dir, $marker_type, $markers_hashref) = @_;
my @marker_type = ();
if ($marker_type eq "SNP") {
push @marker_type, "SNP";
} elsif ($marker_type eq "INDEL") {
push @marker_type, "INDEL";
} elsif ($marker_type eq "BOTH") {
push @marker_type, ("SNP", "INDEL");
} else {
die "Unrecognized marker type: $marker_type! Please input 'SNP' or 'INDEL' or'BOTH'. Exit!\n";
}
foreach my $t (@marker_type) {
# print "extract segregating $t markers ...\n";
my $genome1_based_markers = "$marker_dir/${genome1_tag}-${genome2_tag}.$genome1_tag.final.$t.markers.txt.gz";
my $genome2_based_markers = "$marker_dir/${genome1_tag}-${genome2_tag}.$genome2_tag.final.$t.markers.txt.gz";
unless ((-e $genome1_based_markers) and (-e $genome2_based_markers)) {
die "Cannot find the marker files: $genome1_based_markers and $genome2_based_markers! Exit!\n";
}
my $genome1_based_markers_fh = read_file($genome1_based_markers);
parse_markers_table_file($genome1_based_markers_fh, $genome1_tag, $genome2_tag, $markers_hashref);
close $genome1_based_markers_fh;
my $genome2_based_markers_fh = read_file($genome2_based_markers);
parse_markers_table_file($genome2_based_markers_fh, $genome2_tag, $genome1_tag, $markers_hashref);
close $genome2_based_markers_fh;
}
}
sub parse_markers_table_file {
my ($fh, $ref, $query, $markers_hashref) = @_;
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
/^chr\tstart/ and next;
/^ref_chr\tref_start/ and next;
/^parent1_chr\tparent1_start/ and next;
/^parent2_chr\tparent2_start/ and next;
my ($ref_chr, $ref_start, $ref_end, $ref_allele, $query_allele, $query_chr, $query_start, $query_end, $match_orientation) = split /\t/, $_;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'ref_chr'} = $ref_chr;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'ref_start'} = $ref_start;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'ref_end'} = $ref_end;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'ref_allele'} = $ref_allele;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'query_chr'} = $query_chr;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'query_start'} = $query_start;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'query_end'} = $query_end;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'query_allele'} = $query_allele;
$$markers_hashref{$ref}{$query}{$ref_chr}{$ref_start}{'match_orientation'} = $match_orientation;
}
}
sub parse_mpileup_file {
my ($spore_id, $spore_index, $cross_pair, $ref, $query, $fh, $allow_heteroduplex, $markers_hashref, $genotypes_hashref, $mutations_hashref, $heteroduplex_hashref) = @_;
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
my ($chr, $pos, $ref_allele, $cov, $reads_bases, $reads_quals) = split /\t/, $_;
if (exists $$markers_hashref{$ref}{$query}{$chr}{$pos}) {
my $marker_ref_allele = $$markers_hashref{$ref}{$query}{$chr}{$pos}{'ref_allele'};
my $marker_query_allele = $$markers_hashref{$ref}{$query}{$chr}{$pos}{'query_allele'};
my $marker_ref_allele_length = length $marker_ref_allele;
my $marker_query_allele_length = length $marker_query_allele;
my $marker_type;
if (($marker_ref_allele_length == 1) and ($marker_query_allele_length == 1)) {
$marker_type = "SNP";
} elsif ($marker_ref_allele_length > $marker_query_allele_length) {
$marker_type = "DEL";
} else {
$marker_type = "INS";
}
if ($cov > 0) {
# print "raw mpileup: $_\n";
# remove the start and end marks of reads mapping
$reads_bases =~ s/\^\S//gi;
$reads_bases =~ s/\$//gi;
# print "reads_bases: $reads_bases\n";
my %indels = ();
my $j = 0; # indel index
while ($reads_bases =~ /((?:\S)(?:\+|\-)[0-9]+[ACGTNacgtn]+)/g) {
$j++;
my $indel_raw = $&;
# my $match_start = $-[0] + 1;
# my $match_end = $+[0];
$indels{$j}{'indel_raw'} = $&;
($indels{$j}{'lead_base'}, $indels{$j}{'type'}, $indels{$j}{'length'}, $indels{$j}{'indel_adjusted'}) = ($indels{$j}{'indel_raw'} =~ /(\S)(\+|\-)([0-9]+)([ACGTNacgtn]+)/);
$indels{$j}{'indel_adjusted'} = substr($indels{$j}{'indel_adjusted'}, 0, $indels{$j}{'length'});
if ($indels{$j}{'lead_base'} =~ /(\.|\,)/) {
$indels{$j}{'lead_base'} = $ref_allele;
} else {
# print "corner case! lead_base = $indels{$j}{'lead_base'}\n";
$indels{$j}{'lead_base'} = uc $indels{$j}{'lead_base'};
}
if ($indels{$j}{'type'} eq '+') {
$indels{$j}{'indel_adjusted'} = $indels{$j}{'lead_base'}. $indels{$j}{'indel_adjusted'};
$reads_bases =~ s/(?:\S)(?:\+|\-)[0-9]+[ACGTNacgtn]{$indels{$j}{'length'}}/I/;
} else {
$indels{$j}{'indel_adjusted'} = $indels{$j}{'lead_base'};
$reads_bases =~ s/(?:\S)(?:\+|\-)[0-9]+[ACGTNacgtn]{$indels{$j}{'length'}}/D/;
}
# print "reads_bases after replacement: $reads_bases\n";
}
my %basecall = ();
$j = 0;
for (my $i = 1; $i <= $cov; $i++) {
my $base = substr $reads_bases, $i - 1, 1;
my $qual = substr $reads_quals, $i - 1, 1;
$qual = ord($qual) - 33;
# set safe bound for $qual
if ($qual > 40) {
$qual = 40;
} elsif ($qual < 0) {
$qual = 0;
}
if (($base eq '.') or ($base eq ',')) {
$base = $marker_ref_allele;
} elsif ($base =~ /(I|D)/) {
# if indel
$j++;
$base = uc $indels{$j}{'indel_adjusted'};
} elsif ($base =~ /[ATGCatgc]/) {
$base = uc $base;
} else {
# print "corner case: $base\n";
$base = 'NA';
}
if (not exists $basecall{$base}) {
@{$basecall{$base}{'index'}} = ($i);
@{$basecall{$base}{'qual'}} = ($qual);
$basecall{$base}{'count'} = 1;
} else {
push @{$basecall{$base}{'index'}}, $i;
push @{$basecall{$base}{'qual'}}, $qual;
$basecall{$base}{'count'}++;
}
# print "i=$i: base=$base, basecall_index = @{$basecall{$base}{'index'}}, basecall_qual=@{$basecall{$base}{'qual'}}\n";
}
# print "\n";
foreach my $base (sort keys %basecall) {
$basecall{$base}{'qual_sum'} = cal_sum(@{$basecall{$base}{'qual'}});
}
my @basecall_sorted = sort {$basecall{$b}{'qual_sum'} <=> $basecall{$a}{'qual_sum'} or $basecall{$b}{'count'} <=> $basecall{$a}{'count'}} keys %basecall;
# print "basecall_sorted = @basecall_sorted\n";
my $basecall_major = $basecall_sorted[0];
# print "basecall_major = $basecall_major\n";
my $basecall_major_count = $basecall{$basecall_major}{'count'};
my $basecall_secondary_major;
my $basecall_secondary_major_count = 0;
if ((scalar @basecall_sorted) > 1) {
$basecall_secondary_major = $basecall_sorted[1];
$basecall_secondary_major_count = $basecall{$basecall_secondary_major}{'count'};
}
my $basecall_major_purity = $basecall_major_count/$cov;
my $basecall_secondary_major_purity = $basecall_secondary_major_count/$cov;
# check for potential heteroduplex
my $heteroduplex_flag = 0;
if ($basecall_secondary_major_count > 0) {
if (($basecall_major eq $marker_ref_allele) and ($basecall_secondary_major eq $marker_query_allele)) {
$heteroduplex_flag = 1;
} elsif (($basecall_major eq $marker_query_allele) and ($basecall_secondary_major eq $marker_ref_allele)) {
$heteroduplex_flag = 1;
} else {
$heteroduplex_flag = 0;
}
}
my $basecall_leveraged;
if (($heteroduplex_flag == 1) and ($allow_heteroduplex eq "yes")) {
my $basecall_major_qual_sum = $basecall{$basecall_major}{'qual_sum'};
my $basecall_secondary_major_qual_sum = $basecall{$basecall_secondary_major}{'qual_sum'};
my $basecall_alt_qual_sum = 0;
if (scalar @basecall_sorted > 2 ) {
for(my $b = 2; $b < (scalar @basecall_sorted); $b++) {
my $base = $basecall_sorted[$b];
$basecall_alt_qual_sum += $basecall{$base}{'qual_sum'};
}
}
my $basecall_qual_diff = $basecall_major_qual_sum + $basecall_secondary_major_qual_sum - $basecall_alt_qual_sum;
if (($basecall_qual_diff >= $basecall_qual_diff_cutoff) and ($basecall_major_purity + $basecall_secondary_major_purity >= $basecall_purity_cutoff)) {
$basecall_leveraged = "heteroduplex";
# print "H: $_\n";
# sleep(2);
} else {
$basecall_leveraged = "NA";
}
} else {
my $basecall_major_qual_sum = $basecall{$basecall_major}{'qual_sum'};
my $basecall_alt_qual_sum = 0;
if (scalar @basecall_sorted > 1 ) {
for(my $b = 1; $b < (scalar @basecall_sorted); $b++) {
my $base = $basecall_sorted[$b];
$basecall_alt_qual_sum += $basecall{$base}{'qual_sum'};
}
}
my $basecall_qual_diff = $basecall_major_qual_sum - $basecall_alt_qual_sum;
if (($basecall_qual_diff >= $basecall_qual_diff_cutoff) and ($basecall_major_purity >= $basecall_purity_cutoff)) {
$basecall_leveraged = $basecall_major;
} else {
$basecall_leveraged = "NA";
}
}
# print "basecall_leveraged = $basecall_leveraged, basecall_qual_diff = $basecall_qual_diff\n\n";
if ($basecall_leveraged eq $marker_ref_allele) {
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = $ref;
} elsif ($basecall_leveraged eq $marker_query_allele) {
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = $query;
} elsif ($basecall_leveraged eq 'NA') {
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = "NA";
} elsif ($basecall_leveraged eq 'heteroduplex') {
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = "heteroduplex";
$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_id'} = $spore_id;
$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'cross_pair'} = $cross_pair;
$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'ref_allele'} = $marker_ref_allele;
$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'query_allele'} = $marker_query_allele;
$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_allele'} = "heteroduplex"; # "$basecall_major,$basecall_secondary_major";
} else {
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = "NA";
$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_id'} = $spore_id;
$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'cross_pair'} = $cross_pair;
$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'ref_allele'} = $marker_ref_allele;
$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'query_allele'} = $marker_query_allele;
$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_allele'} = $basecall_leveraged;
}
# print "genotype = $$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}\n\n";
#sleep(2);
} else {
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = "NA";
}
}
}
foreach my $chr (sort keys %{$$markers_hashref{$ref}{$query}}) {
foreach my $pos (sort {$a <=> $b} keys %{$$markers_hashref{$ref}{$query}{$chr}}) {
if (not exists $$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}) {
# print "undifined markers in genotype reading!\n";
# print "chr=$chr, pos=$pos, spore_index=$spore_index\n";
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = "NA";
}
}
}
}
sub filter_genotype_by_cnv {
my ($spore_id, $spore_index, $cross_pair, $ref, $query, $fh, $genotypes_hashref, $mutations_hashref, $heteroduplex_hashref) = @_;
my %cnv = ();
while (<$fh>) {
chomp;
/^#/ and next;
/^\s*$/ and next;
/^chr\tstart\tend\tcopy_number\tstatus\tMWU_test_p_value\tKS_test_p_value/ and next;
my ($chr, $start, $end, $copy_number, $status, $MWU_test_p_value, $KS_test_p_value) = split /\t/, $_;
$cnv{$ref}{$query}{$chr}{$start}{'end'} = $end;
$cnv{$ref}{$query}{$chr}{$start}{'copy_number'} = $copy_number;
$cnv{$ref}{$query}{$chr}{$start}{'status'} = $status;
}
foreach my $chr (sort keys %{$cnv{$ref}{$query}}) {
foreach my $pos (sort {$a <=> $b} keys %{$$genotypes_hashref{$ref}{$query}{$chr}}) {
foreach my $s (sort {$a <=> $b} keys %{$cnv{$ref}{$query}{$chr}}) {
my $e = $cnv{$ref}{$query}{$chr}{$s}{'end'};
if (($pos >= $s) and ($pos <= $e)) {
# print "convert the genotype of $spore_id at $chr:$pos from $$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} to 'NA' due to CNV filter: $chr:$s-$e\n";
$$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index} = "NA";
if (exists $$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}) {
delete $$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index};
}
if (exists $$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}) {
delete $$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index};
}
last;
} elsif ($pos < $s) {
last;
}
}
}
}
}
sub cal_sum {
my @input = @_;
my $sum = 0;
foreach my $n (@input) {
$sum += $n;
}
return $sum;
}
sub infer_genotypes {
my ($genome1_tag, $genome2_tag, $gt_raw_hashref) = @_;
my %allele_count = (
'allele_parent1' => 0,
'allele_parent2' => 0,
'allele_na' => 0,
'allele_mut' => 0,
);
foreach my $spore_index (sort keys %$gt_raw_hashref) {
if ($$gt_raw_hashref{$spore_index} eq $genome1_tag) {
$allele_count{'allele_parent1'}++;
} elsif ($$gt_raw_hashref{$spore_index} eq $genome2_tag) {
$allele_count{'allele_parent2'}++;
} elsif ($$gt_raw_hashref{$spore_index} eq "NA") {
$allele_count{'allele_na'}++;
} else {
$allele_count{'allele_mut'}++;
}
}
# begin inference
my %gt_inferred = %$gt_raw_hashref;
if (($allele_count{'allele_na'} == 1) and ($allele_count{'allele_mut'} == 0)) {
foreach my $spore_index (sort keys %$gt_raw_hashref) {
if ($$gt_raw_hashref{$spore_index} eq "NA") {
if (($allele_count{'allele_parent1'} == 1) and ($allele_count{'allele_parent2'} == 2)) {
$gt_inferred{$spore_index} = $genome1_tag;
} elsif (($allele_count{'allele_parent2'} == 1) and ($allele_count{'allele_parent1'} == 2)) {
$gt_inferred{$spore_index} = $genome2_tag;
} else {
# pass, no inferrence
}
}
}
} elsif (($allele_count{'allele_na'} == 2) and ($allele_count{'allele_mut'} == 0)) {
foreach my $spore_index (sort keys %$gt_raw_hashref) {
if ($$gt_raw_hashref{$spore_index} eq "NA") {
if ($allele_count{'allele_parent1'} == 2) {
$gt_inferred{$spore_index} = $genome2_tag;
} elsif ($allele_count{'allele_parent2'} == 2) {
$gt_inferred{$spore_index} = $genome1_tag;
}
}
}
}
return %gt_inferred;
}
sub crosscheck_genotypes {
my ($tetrad_id, $ref, $query, $markers_hashref, $genotypes_hashref) = @_;
my @spore_indices = qw(a b c d);
my %markers_stat = ();
foreach my $spore_index (@spore_indices) {
$markers_stat{$spore_index}{'total_count'} = 0;
$markers_stat{$spore_index}{'total_cat1_count'} = 0; # genotype resolvable for both parents (i.e. no "NA" calls)
$markers_stat{$spore_index}{'total_cat1_culled'} = 0; # genotype resolvable for both parents but with conflicting calls
$markers_stat{$spore_index}{'total_cat2_count'} = 0; # only parent1 give resolvable genotype
$markers_stat{$spore_index}{'total_cat3_count'} = 0; # only parent2 give resolvable genotype
$markers_stat{$spore_index}{'total_cat4_count'} = 0; # genotype is not resolvale for both parents
}
foreach my $chr_ref (sort keys %{$$markers_hashref{$ref}{$query}}) {
# print "chr=$chr_ref\n";
foreach my $pos_ref (sort {$a <=> $b} keys %{$$markers_hashref{$ref}{$query}{$chr_ref}}) {
my $chr_query = $$markers_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{'query_chr'};
my $pos_query = $$markers_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{'query_start'};
foreach my $spore_index (@spore_indices) {
if (not exists $$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) {
$$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} = "NA";
}
if (not exists $$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}) {
$$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} = "NA";
}
$markers_stat{$spore_index}{'total_count'}++;
if (($$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} ne "NA") and ($$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} ne "NA")) {
$markers_stat{$spore_index}{'total_cat1_count'}++;
if ($$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} ne $$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}) {
# print "conflicting genotypes typeI for spore $tetrad_id.$spore_index, chr_ref = $chr_ref, pos_ref = $pos_ref, chr_query = $chr_query, pos_query = $pos_query >\n";
# print "based on $ref: $$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} ";
# print "based on $query: $$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}\n";
$$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} = "NA";
$$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} = "NA";
$markers_stat{$spore_index}{'total_cat1_culled'}++;
}
} elsif (($$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} ne "NA") and ($$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} eq "NA")) {
$$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} = "NA";
$$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} = "NA";
$markers_stat{$spore_index}{'total_cat2_count'}++;
} elsif (($$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} eq "NA") and ($$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} ne "NA")) {
$$genotypes_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index} = "NA";
$$genotypes_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index} = "NA";
$markers_stat{$spore_index}{'total_cat3_count'}++;
} else {
$markers_stat{$spore_index}{'total_cat4_count'}++;
}
}
}
}
foreach my $spore_index (@spore_indices) {
my $retained_markers_count = $markers_stat{$spore_index}{'total_cat1_count'} - $markers_stat{$spore_index}{'total_cat1_culled'};
my $retaining_pct = (100 * $retained_markers_count)/$markers_stat{$spore_index}{'total_count'};
$retaining_pct = sprintf("%.2f", $retaining_pct);
print "crosscheck_genotypes: spore_id = $tetrad_id.$spore_index, ";
print "total_markers = $markers_stat{$spore_index}{'total_count'}, total_retained_markers = $retained_markers_count, retaining_percentage = $retaining_pct\%\n";
print "total_cat1_markers = $markers_stat{$spore_index}{'total_cat1_count'}, total_cat1_culled = $markers_stat{$spore_index}{'total_cat1_culled'}, total_cat2_markers = $markers_stat{$spore_index}{'total_cat2_count'}, total_cat3_markers = $markers_stat{$spore_index}{'total_cat3_count'}, total_cat4_markers = $markers_stat{$spore_index}{'total_cat4_count'}\n\n";
}
}
sub crosscheck_mutations {
my ($tetrad_id, $ref, $query, $markers_hashref, $mutations_hashref) = @_;
my @spore_indices = qw(a b c d);
foreach my $chr_ref (sort keys %{$$markers_hashref{$ref}{$query}}) {
foreach my $pos_ref (sort {$a <=> $b} keys %{$$markers_hashref{$ref}{$query}{$chr_ref}}) {
my $chr_query = $$markers_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{'query_chr'};
my $pos_query = $$markers_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{'query_start'};
foreach my $spore_index (@spore_indices) {
if ((exists $$mutations_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) and (exists $$mutations_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index})) {
# if the mutation at this marker position have been infered based both parent strains in the same spore, then the mutation confidence score = 1;
$$mutations_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}{'confidence_score'} = 1;
$$mutations_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}{'confidence_score'} = 1;
} elsif ((exists $$mutations_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) and (not exists $$mutations_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index})) {
$$mutations_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}{'confidence_score'} = 0.5;
} elsif ((not exists $$mutations_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) and (exists $$mutations_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index})) {
$$mutations_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}{'confidence_score'} = 0.5;
}
}
}
}
}
sub crosscheck_heteroduplex {
my ($tetrad_id, $ref, $query, $markers_hashref, $heteroduplex_hashref) = @_;
my @spore_indices = qw(a b c d);
foreach my $chr_ref (sort keys %{$$markers_hashref{$ref}{$query}}) {
foreach my $pos_ref (sort {$a <=> $b} keys %{$$markers_hashref{$ref}{$query}{$chr_ref}}) {
my $chr_query = $$markers_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{'query_chr'};
my $pos_query = $$markers_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{'query_start'};
foreach my $spore_index (@spore_indices) {
if ((exists $$heteroduplex_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) and (exists $$heteroduplex_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index})) {
# if the mutation at this marker position have been infered based both parent strains in the same spore, then the mutation confidence score = 1;
$$heteroduplex_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}{'confidence_score'} = 1;
$$heteroduplex_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}{'confidence_score'} = 1;
} elsif ((exists $$heteroduplex_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) and (not exists $$heteroduplex_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index})) {
$$heteroduplex_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}{'confidence_score'} = 0.5;
} elsif ((not exists $$heteroduplex_hashref{$ref}{$query}{$chr_ref}{$pos_ref}{$spore_index}) and (exists $$heteroduplex_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index})) {
$$heteroduplex_hashref{$query}{$ref}{$chr_query}{$pos_query}{$spore_index}{'confidence_score'} = 0.5;
}
}
}
}
}
sub output_genotypes {
my ($prefix, $tetrad_id, $cross_pair, $ref, $query, $chr_arrayref, $genotypes_hashref, $mutations_hashref, $heteroduplex_hashref) = @_;
my $output_for_mutation = "no"; # by default, we turn of this output
my $ref_based_genotypes_detailed_output = "$prefix.genotype.detailed.txt.gz";
my $ref_based_genotypes_detailed_output_fh = write_file($ref_based_genotypes_detailed_output);
print $ref_based_genotypes_detailed_output_fh "tetrad_id\tcross_pair\tref\tchr\tpos\ta_raw_GT\tb_raw_GT\tc_raw_GT\td_raw_GT\ta_inferred_GT\tb_inferred_GT\tc_inferred_GT\td_inferred_GT\n";
my $ref_based_genotypes_lite_raw_output = "$prefix.genotype.lite.raw.txt.gz";
my $ref_based_genotypes_lite_raw_output_fh = write_file($ref_based_genotypes_lite_raw_output);
my $ref_based_genotypes_lite_inferred_output = "$prefix.genotype.lite.inferred.txt.gz";
my $ref_based_genotypes_lite_inferred_output_fh = write_file($ref_based_genotypes_lite_inferred_output);
# my $ref_based_mutation_output = "$prefix.mutations.txt.gz";
# my $ref_based_mutation_output_fh = write_file($ref_based_mutation_output);
# print $ref_based_mutation_output_fh "spore_id\tcross_pair\tref\tchr\tpos\ttype\tref_allele\tquery_allele\tspore_allele\tconfidence_score\n";
my $ref_based_heteroduplex_output = "$prefix.heteroduplex.txt.gz";
my $ref_based_heteroduplex_output_fh = write_file($ref_based_heteroduplex_output);
print $ref_based_heteroduplex_output_fh "spore_id\tcross_pair\tref\tchr\tpos\ttype\tref_allele\tquery_allele\tspore_allele\n";
my @spore_indices = qw(a b c d);
foreach my $c (@$chr_arrayref) {
my $chr = "${ref}_${c}";
foreach my $pos (sort {$a <=> $b} keys %{$$genotypes_hashref{$ref}{$query}{$chr}}) {
my %gt_raw = ();
foreach my $spore_index (@spore_indices) {
if (exists $$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}) {
$gt_raw{$spore_index} = $$genotypes_hashref{$ref}{$query}{$chr}{$pos}{$spore_index};
} else {
$gt_raw{$spore_index} = "NA";
}
# if (exists $$mutations_hashref{$ref}{$query}{$query}{$chr}{$pos}{$spore_index}) {
# # set to >= 1 if want to only report mutations supported by mapping to both parents
# if ($$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'confidence_score'} == 1) {
# print $ref_based_mutation_output_fh "$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_id'}\t";
# print $ref_based_mutation_output_fh "$cross_pair\t$ref\t$chr\t$pos\t";
# print $ref_based_mutation_output_fh "$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'ref_allele'}\t";
# print $ref_based_mutation_output_fh "$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'query_allele'}\t";
# print $ref_based_mutation_output_fh "$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_allele'}\t";
# print $ref_based_mutation_output_fh "$$mutations_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'confidence_score'}\n";
# }
# }
if (exists $$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}) {
if ($$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'confidence_score'} == 1) {
# print "ref=$ref, query=$query, chr=$chr, pos=$pos, spore_index=$spore_index\n";
# print Dumper(\%{$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}});
print $ref_based_heteroduplex_output_fh "$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_id'}\t";
print $ref_based_heteroduplex_output_fh "$cross_pair\t$ref\t$chr\t$pos\t";
print $ref_based_heteroduplex_output_fh "$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'ref_allele'}\t";
print $ref_based_heteroduplex_output_fh "$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'query_allele'}\t";
print $ref_based_heteroduplex_output_fh "$$heteroduplex_hashref{$ref}{$query}{$chr}{$pos}{$spore_index}{'spore_allele'}\n";
}
}
}
my %gt_inferred = infer_genotypes($ref, $query, \%gt_raw);
# generate lite output based on %gt_raw
output_lite($ref_based_genotypes_lite_raw_output_fh, $ref, $query, $chr, $pos, \%gt_raw);
# generate lite output for based on %gt_inferred
output_lite($ref_based_genotypes_lite_inferred_output_fh, $ref, $query, $chr, $pos, \%gt_inferred);
print $ref_based_genotypes_detailed_output_fh "$tetrad_id\t$cross_pair\t$ref\t$chr\t$pos\t";
foreach my $spore_index (@spore_indices) {
print $ref_based_genotypes_detailed_output_fh "$gt_raw{$spore_index}\t";
}
foreach my $spore_index (@spore_indices) {
print $ref_based_genotypes_detailed_output_fh "$gt_inferred{$spore_index}\t";
}
print $ref_based_genotypes_detailed_output_fh "\n";
}
}
}
sub output_lite {
my ($fh, $ref, $query, $chr, $pos, $gt_hashref) = @_;
my @spore_indices = qw(a b c d);
my %gt_lite = ();
my $parent_allele_count = 0;
foreach my $spore_index (@spore_indices) {
if ($$gt_hashref{$spore_index} eq $ref) {
$gt_lite{$spore_index} = $ref;
$parent_allele_count++;
} elsif ($$gt_hashref{$spore_index} eq $query) {
$gt_lite{$spore_index} = $query;
$parent_allele_count++;
} else {
$gt_lite{$spore_index} = $$gt_hashref{$spore_index};
}
}
print $fh "$chr\t$pos\t$ref";
foreach my $spore_index (@spore_indices) {
print $fh "\t$gt_lite{$spore_index}";
}
print $fh "\n";
}