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HLAtypeinference_validation.pl
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#!/usr/bin/perl -w
# ./HLAtypeinference_validation.pl --sampleIDs SRR702070_HapmapExomes_RED --trueHLA /Net/birch/data/dilthey/1000GHLA/SRR1000GGSK_HapMap_combined.txt
# ./HLAtypeinference_validation.pl --sampleIDs NA12878_Platinum_RED --trueHLA /Net/birch/data/dilthey/1000GHLA/G1000_GSK_combined.txt.manuallyAmended
# ./HLAtypeinference_validation.pl --sampleIDs NA12891_Platinum_RED --trueHLA /Net/birch/data/dilthey/1000GHLA/G1000_GSK_combined.txt.manuallyAmended
# ./HLAtypeinference_validation.pl --sampleIDs NA12892_Platinum_RED --trueHLA /Net/birch/data/dilthey/1000GHLA/G1000_GSK_combined.txt.manuallyAmended
# ./HLAtypeinference_validation.pl --sampleIDs all_1000G --trueHLA /Net/birch/data/dilthey/1000GHLA/G1000_GSK_combined.txt.manuallyAmended
# ./HLAtypeinference_validation.pl --sampleIDs withA_NA18939_1000G_RED_FASTQ --trueHLA /Net/birch/data/dilthey/1000GHLA/G1000_GSK_combined.txt.manuallyAmended
# ./HLAtypeinference_validation.pl --sampleIDs NA12878_Platinum_RED,NA12891_Platinum_RED,NA12892_Platinum_RED --trueHLA /Net/birch/data/dilthey/1000GHLA/G1000_GSK_combined.txt.manuallyAmended
use strict;
use List::MoreUtils qw/all mesh any /;
use List::Util qw/sum/;
use Data::Dumper;
use Getopt::Long;
use Sys::Hostname;
use File::Copy;
use File::Basename;
use Storable;
use simpleHLA;
use File::Basename;
my $kMer_size = 55;
# my @testCases = (
# [[qw/A A/], [qw/A A/]],
# [[qw/? A/], [qw/A A/]],
# [[qw/A ?/], [qw/A A/]],
# [[qw/A T/], [qw/A A/]],
# [[qw/A A/], [qw/T A/]],
# [[qw/A C/], [qw/G T/]],
# [[qw/A C/], [qw/? T/]],
# [[qw/? C/], [qw/G T/]],
# [[qw/? ?/], [qw/G T/]],
# [[qw/? T/], [qw/? T/]],
# [[qw/? C/], [qw/? T/]],
# );
# foreach my $testCase (@testCases)
# {
# print join(' vs ', map {join('/', @$_)} @$testCase), " ", join(' ', compatibleStringAlleles($testCase->[0], $testCase->[1])), "\n";
# }
# exit;
# input parameters
my $sampleIDs = '';
my $trueHLA;
my $trueHaplotypes;
my $T = 0;
my $minCoverage = 0;
my $all_2_dig = 0;
my $only_4_dig = 1;
my $reduce_to_4_dig = 0;
my $fromPHLAT = 0;
my $fromHLAreporter = 0;
my $fromKourami = 0;
my @loci_for_check = qw/A B C DQA1 DQB1 DRB1/;
my $exon_folder = qq(../graphs/PRG_MHC_GRCh38_withIMGT/PRG/);
unless(-e $exon_folder)
{
die "Please provide a kMerified graph -- exon folder not there!";
}
GetOptions (
'sampleIDs:s' => \$sampleIDs,
'trueHLA:s' => \$trueHLA,
'trueHaplotypes:s' => \$trueHaplotypes,
#'validation_round:s' => \$validation_round,
'T:s' => \$T,
'minCoverage:s' => \$minCoverage,
'all_2_dig:s' => \$all_2_dig,
'only_4_dig:s' => \$only_4_dig,
'fromPHLAT:s' => \$fromPHLAT,
'fromHLAreporter:s' => \$fromHLAreporter,
'fromKourami:s' => \$fromKourami,
'reduce_to_4_dig:s' => \$reduce_to_4_dig,
);
die if($fromPHLAT and $fromHLAreporter);
die if($fromPHLAT and $fromKourami);
die if($fromHLAreporter and $fromKourami);
if($minCoverage)
{
print "Minimum coverage threshold in place: $minCoverage\n";
}
if($sampleIDs =~ /all_(.+)/)
{
my $searchString = $1;
my @alternatives = glob('../working/*');
@alternatives = grep {(-d $_) and ($_ =~ /$searchString/)} @alternatives;
@alternatives = map {die unless($_ =~ /.+[\\\/](.+)/); $1} @alternatives;
$sampleIDs = join(',', @alternatives);
}
my @sampleIDs = split(/,/, $sampleIDs);
if(@sampleIDs)
{
foreach my $sampleID (@sampleIDs)
{
unless($sampleID =~ /^[\w]+$/)
{
die "Please provide only sample IDs with normal characters.";
}
}
}
my $sample_IDs_abbr;
if($sampleIDs =~ /^allSimulations(_\w+)?/)
{
my $addFilter = $1;
my @dirs;
if($addFilter)
{
@dirs = grep {$_ =~ /I\d+_simulations${addFilter}/} grep {-d $_} glob('../tmp/hla/*');
}
else
{
@dirs = grep {$_ =~ /I\d+_simulations/} grep {-d $_} glob('../tmp/hla/*');
}
@sampleIDs = map {die "Can't parse $_" unless($_ =~ /tmp\/hla\/(.+)/); $1} @dirs;
if($sampleIDs =~ /^all_simulations_I(\d+)/i)
{
my $iteration = $1;
@sampleIDs = grep {$_ =~ /^I${iteration}_/i} @sampleIDs;
}
my $debug = 1;
if($debug)
{
@sampleIDs = grep {die unless($_ =~ /sample(\d+)$/); ($1 < 30)} @sampleIDs;
}
$sample_IDs_abbr = $sampleIDs;
}
elsif($sampleIDs =~ /^all/)
{
my @dirs = grep {$_ !~ /simulations/} grep {-d $_} glob('../tmp/hla/*');
@sampleIDs = map {die "Can't parse $_" unless($_ =~ /tmp\/hla\/(.+)/); $1} @dirs;
if($sampleIDs =~ /^all_I(\d+)/i)
{
my $iteration = $1;
@sampleIDs = grep {$_ =~ /^I${iteration}_/i} @sampleIDs;
}
else
{
die "Does this make sense?";
@sampleIDs = grep {$_ =~ /^$sampleIDs/i} @sampleIDs;
}
$sample_IDs_abbr = $sampleIDs;
}
else
{
$sample_IDs_abbr = join('_', @sampleIDs);
if(length($sample_IDs_abbr) > 50)
{
$sample_IDs_abbr = substr($sample_IDs_abbr, 0, 50);
}
}
my $validation_round = 'R1';
die "Please specify --trueHLA for validation" unless($trueHLA);
# read reference dataset
my %reference_data;
open(REFERENCE, "<", $trueHLA) or die "Cannot open $trueHLA";
my $headerLine = <REFERENCE>;
chomp($headerLine);
$headerLine =~ s/\n//g;
$headerLine =~ s/\r//g;
my @header_fields = split(/[\t ]/, $headerLine);
@header_fields = map {if($_ =~ /HLAD((QA)|(QB)|(RB))$/){$_ .= '1';} $_} @header_fields;
while(<REFERENCE>)
{
my $line = $_;
chomp($line);
$line =~ s/\n//g;
$line =~ s/\r//g;
next unless($line);
my @fields = split(/[\t ]/, $line);
my %line = (mesh @header_fields, @fields);
my $primary_key = $line{'IndividualID'};
$reference_data{$primary_key} = \%line;
}
close(REFERENCE);
# die Dumper(\%reference_data);
my %imputed_HLA;
my %imputed_HLA_Q;
my %imputed_HLA_avgCoverage;
my %imputed_HLA_lowCoverage;
my %imputed_HLA_minCoverage;
my %sample_noI_toI;
my $total_imputations = 0;
my %missing_reference_data;
mkdir('temp');
mkdir('temp/hla_validation');
my $summary_file = 'temp/summary_' . $sample_IDs_abbr . '.txt';
open(SUMMARY, '>', $summary_file) or die "Cannot open $summary_file";
print SUMMARY $sample_IDs_abbr, "\n";
print SUMMARY "\t", join("\t", qw/Locus N CallRate Accuracy/), "\n";
foreach my $sampleID (@sampleIDs)
{
my $sampleID_noI = $sampleID;
$sampleID_noI =~ s/^I\d+_//g;
my $bestGuess_file;
if($fromPHLAT)
{
$bestGuess_file = '/gpfs1/well/gsk_hla/PHLAT/'.$sampleID.'/'.$validation_round.'_bestguess.txt';
unless(-e $bestGuess_file)
{
warn "Best-guess file $bestGuess_file not existing";
next;
}
}
elsif($fromHLAreporter)
{
$bestGuess_file = '/gpfs1/well/gsk_hla/HLAreporter/results/'.$sampleID.'/'.$validation_round.'_bestguess.txt';
unless(-e $bestGuess_file)
{
warn "Best-guess file $bestGuess_file not existing";
next;
}
}
elsif($fromKourami)
{
$bestGuess_file = '/data/projects/phillippy/projects/MHC/HLA-PRG-LA/fromKourami/' . $sampleID . '/KouramiHLA.txt';
unless(-e $bestGuess_file)
{
warn "Best-guess file $bestGuess_file not existing";
next;
}
}
else
{
$bestGuess_file = '../working/'.$sampleID.'/hla/'.$validation_round.'_bestguess.txt';
unless(-e $bestGuess_file)
{
warn "Best-guess file $bestGuess_file not existing";
next;
}
}
open(BESTGUESS, '<', $bestGuess_file) or die "Cannot open $bestGuess_file";
my $bestguess_header_line = <BESTGUESS>;
chomp($bestguess_header_line);
my @bestguess_header_files = split(/\t/, $bestguess_header_line);
while(<BESTGUESS>)
{
my $line = $_;
chomp($line);
my @line_fields = split(/\t/, $line);
my %line_hash = (mesh @bestguess_header_files, @line_fields);
my $Q = $line_hash{'Q1'};
$imputed_HLA_Q{$line_hash{'Locus'}}{$sampleID_noI}{$line_hash{'Chromosome'}} = $Q;
if($Q < $T)
{
$imputed_HLA{$line_hash{'Locus'}}{$sampleID_noI}{$line_hash{'Chromosome'}} = '??:??';
}
else
{
die unless(defined $line_hash{'Allele'});
$imputed_HLA{$line_hash{'Locus'}}{$sampleID_noI}{$line_hash{'Chromosome'}} = $line_hash{'Allele'};
}
$total_imputations++;
if($line_hash{'Chromosome'} eq '1')
{
$imputed_HLA_avgCoverage{$line_hash{'Locus'}}{$sampleID_noI} = $line_hash{'AverageCoverage'};
$imputed_HLA_lowCoverage{$line_hash{'Locus'}}{$sampleID_noI} = $line_hash{'CoverageFirstDecile'};
$imputed_HLA_minCoverage{$line_hash{'Locus'}}{$sampleID_noI} = $line_hash{'MinimumCoverage'};
if($minCoverage and ($line_hash{'MinimumCoverage'} < $minCoverage))
{
$imputed_HLA{$line_hash{'Locus'}}{$sampleID_noI}{$line_hash{'Chromosome'}} = '??:??';
}
}
}
close(BESTGUESS);
die if(exists $sample_noI_toI{$sampleID_noI});
$sample_noI_toI{$sampleID_noI} = $sampleID;
}
print "\nTotal imputations (for comparisons): ", $total_imputations, "\n";
my $debug = 0;
my $comparisons = 0;
my $compare_problems = 0;
my %locus_avgCoverages;
my %locus_lowCoverages;
my %locus_minCoverages;
my @allLoci_allIndivs_avgCoverage;
my %problem_locus_detail;
my %problem_locus_examined;
my %problem_haplo_counter;
my %problem_haplo_detail;
my %imputations_predictions;
my %reference_predictions;
my %imputed_HLA_Calls;
my %quality_measures; # not used
my $pileup_href = {};
# die Dumper(\%imputed_HLA);
my @loci = sort keys %imputed_HLA;
# die Dumper(\@loci);
my $process_quality_measures = sub {};
my $PP_to_basket = sub {
my $PP = shift;
die unless(($PP >= 0) && ($PP <= 1));
my $basket = int($PP * 10);
$basket = 9 if($basket == 10);
return $basket;
};
my %types_as_validated;
foreach my $locus (@loci)
{
my $arbitraty_indiv = (keys %reference_data)[0];
next unless((defined $reference_data{$arbitraty_indiv}{'HLA'.$locus}));
my %calibration_baskets;
my %coverage_over_samples;
my %coverage_over_samples_individualValues;
my $coverage_over_samples_nSamples = 0;
my $add_to_calibration_basket = sub {
my $str_correct = shift;
my $PP = shift;
my $weight = shift;
die unless(($str_correct eq 'correct') or ($str_correct eq 'incorrect'));
die unless(defined $PP);
die unless(defined $weight);
push(@{$calibration_baskets{$PP_to_basket->($PP)}{$str_correct}}, {PP => $PP, weight => $weight});
};
$problem_locus_examined{$locus} = 0;
$problem_locus_detail{$locus} = 0;
my @indivIDs = keys %{$imputed_HLA{$locus}};
my $indivI_processedForEvaluation = -1;
INDIV: foreach my $indivID (@indivIDs)
{
$| = 1;
# print "\t", $indivID, "\t", $locus, "\n";
$debug = 0;
my @imputed_hla_values = map { $imputed_HLA{$locus}{$indivID}{$_} } keys %{$imputed_HLA{$locus}{$indivID}};
if(grep {simpleHLA::autoHLA_is2digit($_)} @imputed_hla_values)
{
die "Warning: 2-digit alleles detected in the inference set\n" . Dumper(\@imputed_hla_values); # 2-digit test
}
my @imputed_hla_values_q = map { my $r = $imputed_HLA_Q{$locus}{$indivID}{$_}; die unless(defined $r); $r } keys %{$imputed_HLA{$locus}{$indivID}};
die "Undefined HLA ".join(', ', @imputed_hla_values) unless(scalar(grep {defined $_} @imputed_hla_values) == scalar(@imputed_hla_values));
my @reference_hla_values;
next INDIV unless($#imputed_hla_values == 1);
my $reference_lookup_ID = $indivID;
if($reference_lookup_ID =~ /^withA_/)
{
$reference_lookup_ID =~ s/withA_//;
}
if($reference_lookup_ID =~ /_FASTQ$/)
{
$reference_lookup_ID =~ s/_FASTQ$//;
}
if($reference_lookup_ID =~ /^downsample_/)
{
$reference_lookup_ID =~ s/^downsample_(I\d+_)?//;
$reference_lookup_ID =~ s/_DSC\d+_\d+//;
}
if($reference_lookup_ID =~ /^C_Platinum_/)
{
$reference_lookup_ID =~ s/C_Platinum_//;
}
if($reference_lookup_ID =~ /^Platinum_/)
{
$reference_lookup_ID =~ s/Platinum_//;
}
if($reference_lookup_ID =~ /_1000G/i)
{
$reference_lookup_ID =~ s/_1000G//i;
}
if($reference_lookup_ID =~ /1000G_/i)
{
$reference_lookup_ID =~ s/1000G_//i;
}
if($reference_lookup_ID =~ /_PLATINUM/i)
{
$reference_lookup_ID =~ s/_PLATINUM//i;
}
if($reference_lookup_ID =~ /_HapmapExomes/i)
{
$reference_lookup_ID =~ s/_HapmapExomes//i;
}
if($reference_lookup_ID =~ /_RED/i)
{
$reference_lookup_ID =~ s/_RED//i;
}
if($reference_lookup_ID =~ /_PacBio/i)
{
$reference_lookup_ID =~ s/_PacBio//i;
}
if($reference_lookup_ID =~ /_Nanopore/i)
{
$reference_lookup_ID =~ s/_Nanopore//i;
}
unless(exists $reference_data{$reference_lookup_ID})
{
$missing_reference_data{$reference_lookup_ID}{$locus}++;
# warn "No reference data for $locus $indivID";
}
next INDIV unless(exists $reference_data{$reference_lookup_ID});
$reference_data{$reference_lookup_ID}{'HLA'.$locus} or die;
if($reference_data{$reference_lookup_ID}{'HLA'.$locus})
{
@reference_hla_values = split(/\//, $reference_data{$reference_lookup_ID}{'HLA'.$locus});
}
$types_as_validated{$reference_lookup_ID}{$locus} = \@reference_hla_values;
die Dumper($reference_data{$reference_lookup_ID}, \@reference_hla_values) unless($#reference_hla_values == 1);
die "Undefined HLA ".join(', ', @reference_hla_values) unless(scalar(grep {defined $_} @reference_hla_values) == scalar(@reference_hla_values));
@reference_hla_values = grep {! &simpleHLA::modernHLA_is_missing($_)} @reference_hla_values;
if($#reference_hla_values == -1)
{
$missing_reference_data{$reference_lookup_ID}{$locus}++;
next;
}
if($only_4_dig)
{
next unless (&simpleHLA::HLA_is4digit($reference_hla_values[0]) and (($#reference_hla_values == 0) || (&simpleHLA::HLA_is4digit($reference_hla_values[1]))));
}
if($reduce_to_4_dig)
{
my @reference_hla_values_before = @reference_hla_values;
@reference_hla_values = map {
my @inputAlleles = split(/;/, $_);
join(';', map {simpleHLA::HLA_4digit($_)} @inputAlleles)
} @reference_hla_values;
print "Before:\n\t".join(' / ', @reference_hla_values_before), "\n";
print "After:\n\t".join(' / ', @reference_hla_values), "\n\n";
}
$imputed_HLA_Calls{$locus}{sum} += scalar(@imputed_hla_values);
$indivI_processedForEvaluation++;
my @imputed_present = map {(! &simpleHLA::is_missing($_)) ? 1 : 0} @imputed_hla_values;
my @imputed_hla_values_q_new;
for(my $i = 0; $i <= $#imputed_hla_values; $i++)
{
my $Q = $imputed_hla_values_q[$i];
die unless(defined $Q);
die unless(defined $imputed_present[$i]);
if($imputed_present[$i])
{
push(@imputed_hla_values_q_new, $Q);
}
}
@imputed_hla_values = grep {! &simpleHLA::is_missing($_)} @imputed_hla_values;
@imputed_hla_values_q = @imputed_hla_values_q_new;
die unless($#imputed_hla_values == $#imputed_hla_values_q);
$imputed_HLA_Calls{$locus}{called} += scalar(@imputed_hla_values);
if($indivID =~ /wtsi/i)
{
my @imp_before = @imputed_hla_values;
@imputed_hla_values = map {my @alleles = split(/;/, $_); join(';', map {($_ =~ /[GNLQ]$/) ? ($_) : ($_, $_ . ':01', $_ . ':01:01', )} @alleles)} @imputed_hla_values;
#die Dumper(\@imp_before, \@imputed_hla_values);
}
if($all_2_dig)
{
@reference_hla_values = map {join(';', map {&simpleHLA::autoHLA_2digit($_)} split(/;/, $_))} @reference_hla_values;
@imputed_hla_values = map {join(';', map {&simpleHLA::autoHLA_2digit($_)} split(/;/, $_))} @imputed_hla_values;
}
if($locus eq 'B')
{
# print Dumper($indivID, \@reference_hla_values, \@imputed_hla_values), "\n";
}
my $comparisons_before = $comparisons;
my $problem_locus_detail_before = $problem_locus_detail{$locus};
if($#imputed_hla_values == 1)
{
if($#reference_hla_values > -1)
{
if($#reference_hla_values == 0)
{
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]) or &compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[1]))
{
$comparisons++;
$problem_locus_examined{$locus}++;
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]))
{
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
}
elsif(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[1]))
{
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{correct}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[1], 1);
}
$process_quality_measures->($locus, $quality_measures{$indivID}, 1, 1);
}
else
{
$comparisons++;
$compare_problems++;
$problem_haplo_counter{$indivID}++;
$problem_haplo_detail{$indivID}{$locus} = 'Reference: '.join('/', @reference_hla_values).' VS Imputed: '.join('/', @imputed_hla_values).' (1 problem of 1)';
$problem_locus_detail{$locus}++;
$problem_locus_examined{$locus}++;
$reference_predictions{$locus}{$reference_hla_values[0]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{incorrect} += 0.5;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{incorrect} += 0.5;
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[0], 0.5);
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[1], 0.5);
$process_quality_measures->($locus, $quality_measures{$indivID}, 0, 1);
}
}
elsif($#reference_hla_values == 1)
{
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]) and &compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[1]))
{
$comparisons += 2;
$problem_locus_examined{$locus} += 2;
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$reference_predictions{$locus}{$reference_hla_values[1]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{correct}++;
$process_quality_measures->($locus, $quality_measures{$indivID}, 2, 2);
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
$add_to_calibration_basket->('correct', $imputed_hla_values_q[1], 1);
}
elsif(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[1]) and &compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[0]))
{
$comparisons += 2;
$problem_locus_examined{$locus} += 2;
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$reference_predictions{$locus}{$reference_hla_values[1]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{correct}++;
$process_quality_measures->($locus, $quality_measures{$indivID}, 2, 2);
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
$add_to_calibration_basket->('correct', $imputed_hla_values_q[1], 1);
}
else
{
if(
&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]) or &compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[1]) or
&compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[0]) or &compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[1])
)
{
$comparisons += 2;
$compare_problems++;
$problem_haplo_counter{$indivID}++;
$problem_haplo_detail{$indivID}{$locus} = 'Reference: '.join('/', @reference_hla_values).' VS Imputed: '.join('/', @imputed_hla_values).' (1 problem of 2)';
$problem_locus_detail{$locus}++;
$problem_locus_examined{$locus} += 2;
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]))
{
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$reference_predictions{$locus}{$reference_hla_values[1]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{incorrect}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[1], 1);
}
elsif(&compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[1]))
{
$reference_predictions{$locus}{$reference_hla_values[1]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{correct}++;
$reference_predictions{$locus}{$reference_hla_values[0]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{incorrect}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[1], 1);
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[0], 1);
}
elsif(&compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[0]))
{
$reference_predictions{$locus}{$reference_hla_values[1]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$reference_predictions{$locus}{$reference_hla_values[0]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{incorrect}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[1], 1);
}
elsif(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[1]))
{
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{correct}++;
$reference_predictions{$locus}{$reference_hla_values[1]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{incorrect}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[1], 1);
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[0], 1);
}
$process_quality_measures->($locus, $quality_measures{$indivID}, 1, 2);
}
else
{
$comparisons += 2;
$compare_problems += 2;
$problem_haplo_counter{$indivID} += 2;
$problem_haplo_detail{$indivID}{$locus} = 'Reference: '.join('/', @reference_hla_values).' VS Imputed: '.join('/', @imputed_hla_values).' (2 problems of 2)';
$problem_locus_detail{$locus} += 2;
$problem_locus_examined{$locus} += 2;
$reference_predictions{$locus}{$reference_hla_values[0]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{incorrect}++;
$reference_predictions{$locus}{$reference_hla_values[1]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[1]}{incorrect}++;
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[0], 1);
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[1], 1);
$process_quality_measures->($locus, $quality_measures{$indivID}, 0, 2);
}
}
}
else
{
die;
}
}
}
elsif($#imputed_hla_values == 0)
{
if($#reference_hla_values > -1)
{
if($#reference_hla_values == 0)
{
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]))
{
$comparisons++;
$problem_locus_examined{$locus}++;
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
$process_quality_measures->($locus, $quality_measures{$indivID}, 1, 1);
}
else
{
$comparisons++;
$compare_problems++;
$problem_haplo_counter{$indivID}++;
$problem_haplo_detail{$indivID}{$locus} = 'Reference: '.join('/', @reference_hla_values).' VS Imputed: '.join('/', @imputed_hla_values).' (1 problem of 1)';
$problem_locus_detail{$locus}++;
$problem_locus_examined{$locus}++;
$reference_predictions{$locus}{$reference_hla_values[0]}{incorrect}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{incorrect}++;
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[0], 1);
$process_quality_measures->($locus, $quality_measures{$indivID}, 0, 1);
}
}
elsif($#reference_hla_values == 1)
{
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]) or &compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[0]))
{
$comparisons += 1;
$problem_locus_examined{$locus} += 1;
if(&compatibleAlleles_individual($locus, $reference_hla_values[0], $imputed_hla_values[0]))
{
$reference_predictions{$locus}{$reference_hla_values[0]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
}
elsif(&compatibleAlleles_individual($locus, $reference_hla_values[1], $imputed_hla_values[0]))
{
$reference_predictions{$locus}{$reference_hla_values[1]}{correct}++;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{correct}++;
$add_to_calibration_basket->('correct', $imputed_hla_values_q[0], 1);
}
$process_quality_measures->($locus, $quality_measures{$indivID}, 1, 1);
}
else
{
$comparisons++;
$compare_problems++;
$problem_haplo_counter{$indivID}++;
$problem_haplo_detail{$indivID}{$locus} = 'Reference: '.join('/', @reference_hla_values).' VS Imputed: '.join('/', @imputed_hla_values).' (1 problem of 1)';
$problem_locus_detail{$locus}++;
$problem_locus_examined{$locus}++;
$reference_predictions{$locus}{$reference_hla_values[0]}{incorrect} += 0.5;
$reference_predictions{$locus}{$reference_hla_values[1]}{incorrect} += 0.5;
$imputations_predictions{$locus}{$imputed_hla_values[0]}{incorrect}++;
$add_to_calibration_basket->('incorrect', $imputed_hla_values_q[0], 1);
$process_quality_measures->($locus, $quality_measures{$indivID}, 0, 1);
}
}
else
{
die;
}
}
}
my $thisIndiv_problems = $problem_locus_detail{$locus} - $problem_locus_detail_before;
my $avgCoverage = $imputed_HLA_avgCoverage{$locus}{$indivID};
my $lowCoverage = $imputed_HLA_lowCoverage{$locus}{$indivID};
my $minCoverage = $imputed_HLA_minCoverage{$locus}{$indivID};
# average coverages
if(($thisIndiv_problems > 0))
{
push(@{$locus_avgCoverages{$locus}{problems}}, $avgCoverage);
push(@{$locus_lowCoverages{$locus}{problems}}, $lowCoverage);
push(@{$locus_minCoverages{$locus}{problems}}, $minCoverage);
}
else
{
push(@{$locus_avgCoverages{$locus}{ok}}, $avgCoverage);
push(@{$locus_lowCoverages{$locus}{ok}}, $lowCoverage);
push(@{$locus_minCoverages{$locus}{ok}}, $minCoverage);
}
push (@allLoci_allIndivs_avgCoverage, $avgCoverage);
# print "\t", $thisIndiv_problems, "\n";
# just for debugging - deactivated
if($thisIndiv_problems == 0)
{
if($locus eq 'A')
{
# print join(' vs ', join('/', @reference_hla_values), join('/', @imputed_hla_values)), "\n";
}
}
my $thisIndiv_comparions = $comparisons - $comparisons_before;
my $thisIndiv_OK = $thisIndiv_comparions - $thisIndiv_problems;
my $indivID_withI = $sample_noI_toI{$indivID};
die unless(defined $indivID_withI);
my $pileup_file = qq(../working/$indivID_withI/hla/${validation_round}_pileup_${locus}.txt);
my $coverages_href = load_coverages_from_pileup($pileup_file);
my @k_coverages_existing;
if($indivI_processedForEvaluation > 0)
{
foreach my $exon (keys %coverage_over_samples)
{
foreach my $exonPos (keys %{$coverage_over_samples{$exon}})
{
push(@k_coverages_existing, $exon . '-/-' . $exonPos);
}
}
}
my @k_coverages_thisSample;
foreach my $exon (keys %$coverages_href)
{
foreach my $exonPos (keys %{$coverages_href->{$exon}})
{
$coverage_over_samples{$exon}{$exonPos} += $coverages_href->{$exon}{$exonPos};
push(@{$coverage_over_samples_individualValues{$exon}{$exonPos}}, $coverages_href->{$exon}{$exonPos});
push(@k_coverages_thisSample, $exon . '-/-' . $exonPos);
}
}
$coverage_over_samples_nSamples++;
if($indivI_processedForEvaluation > 0)
{
my ($n_shared, $aref_l1_excl, $aref_l2_excl) = list_comparison(\@k_coverages_existing, \@k_coverages_thisSample);
if(($#{$aref_l1_excl} == -1) and ($#{$aref_l2_excl} == -1))
{
die unless($n_shared == scalar(@k_coverages_existing));
die unless($n_shared == scalar(@k_coverages_thisSample));
}
else
{
warn Dumper("There is a problem with per-exon coverage numbers.", $indivI_processedForEvaluation, scalar(@k_coverages_existing), scalar(@k_coverages_thisSample), scalar(@$aref_l1_excl), scalar(@$aref_l2_excl));
}
}
if($thisIndiv_problems)
{
print join("\t", $indivID, $locus, $thisIndiv_problems . ' problems', "Reference " . $reference_data{$reference_lookup_ID}{'HLA'.$locus}, "Inference " . join('/', @imputed_hla_values)), "\n";
}
if(($thisIndiv_problems > 0) and (not $all_2_dig) and not ($fromPHLAT) and not($fromHLAreporter) and not($fromKourami) and (not ($indivID) =~ /wtsi/i))
{
my %readIDs;
unless(-e $pileup_file)
{
die "Can't find pileup file $pileup_file";
}
load_pileup($pileup_href, $pileup_file, $indivID_withI);
my $output_fn = 'temp/hla_validation/pileup_'.$validation_round.'_'.$indivID_withI.'_'.$locus.'.txt';
open(my $output_fh, '>', $output_fn) or die "Cannot open $output_fn";
print $output_fh join("\t", $indivID_withI, $locus, $thisIndiv_OK), "\n";
unless(scalar(@imputed_hla_values) == 2)
{
warn "Can't produce pileup for $locus / $indivID";
next;
}
my $inferred = \@imputed_hla_values;
my $truth = \@reference_hla_values;
if(scalar( grep {$_ =~ /XX/} @$truth) > 0)
{
warn "Can't produce pileup for $locus / $indivID";
next;
}
print {$output_fh} $inferred->[0], "\t\t\t", $truth->[0], "\n";
print {$output_fh} $inferred->[1], "\t\t\t", $truth->[1], "\n\n";
print {$output_fh} join("\t", "Inferred", "", "", "Apparently true", ""), "\n";
my @exons = print_which_exons($locus);
my @inferred_trimmed = twoClusterAlleles($inferred);
foreach my $exon (@exons)
{
my $file = find_exon_file($locus, $exon);
my $sequences = read_exon_sequences($file);
my @validated_extended = twoValidationAlleles_2_proper_names($truth, $locus, $sequences);
my $oneAllele = (keys %$sequences)[0];
my $length = length($sequences->{$oneAllele});
# print "-", $sequences->{$oneAllele}, "-\n\n";
die Dumper("Truth alleles not equal to 2?", \@validated_extended) unless(scalar(grep {$sequences->{$_}} @validated_extended) == 2);
die unless(scalar(grep {$sequences->{$_}} @inferred_trimmed) == 2);
print {$output_fh} join("\t",
$inferred_trimmed[0].' Exon '.$exon,
$inferred_trimmed[1].' Exon '.$exon,
"",
$validated_extended[0].' Exon '.$exon,
$validated_extended[1].' Exon '.$exon,
), "\n";
# print Dumper($locus, [keys %{$pileup_href->{$indivID_withI}}]);
for(my $i = 0; $i < $length; $i++)
{
my @chars_for_print;
push(@chars_for_print, map {substr($sequences->{$_}, $i, 1)} @inferred_trimmed);
push(@chars_for_print, '');
push(@chars_for_print, map {substr($sequences->{$_}, $i, 1)} @validated_extended);
if($chars_for_print[0] ne $chars_for_print[1])
{
$chars_for_print[2] = '!';
}
if($chars_for_print[0] ne $chars_for_print[3])
{
$chars_for_print[5] = '!';
}
else
{
$chars_for_print[5] = '';
}
if($chars_for_print[1] ne $chars_for_print[4])
{
$chars_for_print[6] = '!';
}
else
{
$chars_for_print[6] = '';
}
if(exists $pileup_href->{$indivID_withI}{'HLA'.$locus})
{
my $pileUpString = $pileup_href->{$indivID_withI}{'HLA'.$locus}[$exon-2][$i];
die unless(defined $pileup_href->{$indivID_withI});
die unless(defined $pileup_href->{$indivID_withI}{'HLA'.$locus});
die unless(defined $pileup_href->{$indivID_withI}{'HLA'.$locus}[$exon-2]);
# die "Problem with pileup for $locus / $indivID / $exon / $i " unless(defined $pileUpString);
# next unless(defined $pileUpString);
my %idt_per_allele;
my $pileUpString_forSplit = $pileUpString;
#my $pileUpString_forSplit = 'GGGGAAATACCTCAGGGAGT (35, 35, 35, 61, 62, 57, 52, 41, 56, 49, 46, 52, 42, 45, 36, 52, 51, 51, 56, 56) ';
$pileUpString_forSplit =~ s/\([\d\s,]+\)/()/g;
#die $pileUpString_forSplit;
my @pileUpString_parts = split(/,/, $pileUpString_forSplit);
my @all_alleles;
my @all_identities;
foreach my $element (@pileUpString_parts)
{
die Dumper("Weird element", $element, \@pileUpString_parts, $pileUpString_forSplit) unless($element =~ /(\S+) \(\d*\) \[(.+)\]/);
my $allele = $1;
my $details = $2;
# e.g. 198 | 1 | 1 1 | 1 0.983762 |
die "Weird details string $details" unless($details =~ /pairsDistance ([\-\d]+) \| alignmentLength ([\d]+) \| ([\d\.]+) \| ([\d\.]+) ([\d\.]+) \| ([\d\.]+) ([\-\d\.]+) \| /);