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Copy pathvcf_gq_dp_missing_data.pl
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199 lines (179 loc) · 7.17 KB
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Copy pathvcf_gq_dp_missing_data.pl
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199 lines (179 loc) · 7.17 KB
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sub process {
my ( $vcf_line, $sample_names_ref, $data_ref ) = @_;
chomp $vcf_line;
my $dp_max = 99;
my $gq_max = 99;
my @fields = split /\t/, $vcf_line;
my %position;
my @format_fields = split /:/, $fields[8];
my $gt_field_num = -1;
my $gq_field_num = -1;
my $dp_field_num = -1;
for my $i ( 0 .. ( @format_fields - 1 ) ) {
if ( $format_fields[$i] eq "GT" ) { $gt_field_num = $i; }
if ( $format_fields[$i] eq "GQ" ) { $gq_field_num = $i; }
if ( $format_fields[$i] eq "DP" ) { $dp_field_num = $i; }
}
my $missing = 0;
my %pos_dp_filter;
my %pos_gq_filter;
for my $i ( 9 .. ( @{$sample_names_ref} + 8 ) ) {
if ( $fields[$i] eq "./." ) {
$data_ref->{stat}{dp}{ $sample_names_ref->[ $i - 9 ] }{0}++;
$data_ref->{stat}{gq}{ $sample_names_ref->[ $i - 9 ] }{0}++;
}
else {
my @sample_f = split /:/, $fields[$i];
# At threshold $_, increment the number of individuals present for this position;
# individual will be filtered at every threshold above its own depth/quality
map { $pos_dp_filter{$_}++ }
( 0 .. ($sample_f[$dp_field_num] < $dp_max ? $sample_f[$dp_field_num] - 1 : $dp_max) );
map { $pos_gq_filter{$_}++ }
( 0 .. ($sample_f[$gq_field_num] < $gq_max ? $sample_f[$gq_field_num] - 1 : $gq_max) );
$data_ref->{stat}{dp}{ $sample_names_ref->[ $i - 9 ] }
{ $sample_f[$dp_field_num] }++;
$data_ref->{stat}{gq}{ $sample_names_ref->[ $i - 9 ] }
{ $sample_f[$gq_field_num] }++;
$data_ref->{range}{dp}{ $sample_f[$dp_field_num] }++;
$data_ref->{range}{gq}{ $sample_f[$gq_field_num] }++;
}
}
# At threshold $_, $pos_xx_filter{$_} individuals would be present at this position, which is on scaffold $fields[0]
map {
$data_ref->{present}{dp}{$_}{ $pos_dp_filter{$_} }{ $fields[0] }++
} keys %pos_dp_filter;
map {
$data_ref->{present}{gq}{$_}{ $pos_gq_filter{$_} }{ $fields[0] }++
} keys %pos_gq_filter;
return;
}
sub merge {
my ($data_ref, $final_ref) = @_;
if ( defined($data_ref) ) {
foreach my $stat ( keys %{ $data_ref->{present} } ) {
foreach my $threshold ( keys %{ $data_ref->{present}{$stat} } )
{
foreach my $missing_ind (
keys %{ $data_ref->{present}{$stat}{$threshold} } )
{
foreach my $scf (
keys %{
$data_ref->{present}{$stat}{$threshold}
{$missing_ind}
}
)
{
$final_ref->{present}{$stat}{$threshold}
{$missing_ind}{$scf} +=
$data_ref->{present}{$stat}{$threshold}
{$missing_ind}{$scf};
}
}
}
}
foreach my $stat ( keys %{ $data_ref->{stat} } ) {
foreach my $sample_name ( keys %{ $data_ref->{stat}{$stat} } ) {
foreach my $val (
keys %{ $data_ref->{stat}{$stat}{$sample_name} } )
{
$final_ref->{stat}{$stat}{$sample_name}{$val} +=
$data_ref->{stat}{$stat}{$sample_name}{$val};
}
}
}
foreach my $stat ( keys %{ $data_ref->{range} } ) {
foreach my $val ( keys %{ $data_ref->{range}{$stat} } ) {
$final_ref->{range}{$stat}{$val} +=
$data_ref->{range}{$stat}{$val};
}
}
}
}
sub output {
my ( $final_data_ref, $scflen_ref, $sample_names_ref, $genome_length, $output_prefix ) = @_;
foreach my $stat ( "dp", "gq" ) {
open my $stat_file, ">", "$output_prefix.sample.$stat.txt" or croak "Can't open $output_prefix.sample.$stat.txt\n";
print $stat_file "Ind\\$stat";
foreach my $stat_val (
sort { $a <=> $b }
keys %{ $final_data_ref->{range}{$stat} }
)
{
print $stat_file "\t$stat_val";
}
print $stat_file "\n";
foreach my $sample (
sort { $a <=> $b }
keys %{ $final_data_ref->{stat}{$stat} }
)
{
print $stat_file "$sample";
foreach my $stat_val (
sort { $a <=> $b }
keys %{ $final_data_ref->{range}{$stat} }
)
{
if (
defined $final_data_ref->{stat}{$stat}{$sample}{$stat_val} )
{
print $stat_file
"\t$final_data_ref->{stat}{$stat}{$sample}{$stat_val}";
}
else {
print $stat_file "\t0";
}
}
print $stat_file "\n";
}
close $stat_file;
}
open my $present_file, ">", "$output_prefix.present.txt" or croak "Can't open $output_prefix.present.txt\n";
print $present_file "Stat\tThreshold\tSamples\tBases\tCumulative.Bases\tCumulative.Scaffolds\tCumulative.Scaffold.pc\tGenome.Coverage\tGenome.Coverage.pc\n";
foreach my $stat ( sort keys %{ $final_data_ref->{present} } ) {
foreach my $threshold (
sort { $a <=> $b }
keys %{ $final_data_ref->{present}{$stat} }
)
{
my $cumul_bases = 0;
my %cumul_scf;
foreach my $present_ind ( reverse 1 .. @{$sample_names_ref} ) {
my $bases_w_ind_present = 0;
if (
defined $final_data_ref->{present}{$stat}{$threshold}
{$present_ind} )
{
foreach my $scf (
keys %{
$final_data_ref->{present}{$stat}{$threshold}
{$present_ind}
}
)
{
$bases_w_ind_present +=
$final_data_ref->{present}{$stat}{$threshold}
{$present_ind}{$scf};
$cumul_bases +=
$final_data_ref->{present}{$stat}{$threshold}
{$present_ind}{$scf};
$cumul_scf{$scf}++;
}
}
my $base_coverage = 0;
foreach my $scf ( keys %cumul_scf ) {
$base_coverage += $scflen_ref->{$scf};
}
my $pc_base_coverage = sprintf "%5.2f",
$base_coverage / $genome_length * 100;
my $cumul_scf_num = keys %cumul_scf;
my $pc_scfs = sprintf "%5.2f",
$cumul_scf_num / keys( %{$scflen_ref} ) * 100;
print $present_file
"$stat\t$threshold\t$present_ind\t$bases_w_ind_present\t$cumul_bases\t$cumul_scf_num\t$pc_scfs\t$base_coverage\t$pc_base_coverage\n";
}
}
}
close $present_file;
return;
}
1; # Needed to return a true value when imported by vcf-parallel