vcftools 0.1.11+dfsg-1 / usr / bin / vcf-fix-ploidy

#!/usr/bin/env perl
#
# Author: petr.danecek@sanger
#

use strict;
use warnings;
use Carp;
use Vcf;

my $opts = parse_params();
fix_ploidy($opts);

exit;

#--------------------------------

sub error
{
    my (@msg) = @_;
    if ( scalar @msg ) { confess @msg; }
    print 
        "Usage: cat broken.vcf | vcf-fix-ploidy [OPTIONS] > fixed.vcf\n",
        "Options:\n",
        "   -a, --assumed-sex <sex>         M or F, required if the list is not complete in -s\n",
        "   -l, --fix-likelihoods           Add or remove het likelihoods (not the default behaviour)\n",
        "   -p, --ploidy <file>             Ploidy definition. The default is shown below.\n",
        "   -s, --samples <file>            List of sample sexes (sample_name [MF]).\n",
        "   -h, -?, --help                  This help message.\n",
        "Default ploidy definition:\n",
        "   ploidy =>\n",
        "   {\n",
        "       X =>\n",
        "       [\n",
        "           # The pseudoautosomal regions 60,001-2,699,520 and 154,931,044-155,270,560 with the ploidy 2\n",
        "           { from=>1, to=>60_000, M=>1 },\n",
        "           { from=>2_699_521, to=>154_931_043, M=>1 },\n",
        "       ],\n",
        "       Y =>\n",
        "       [\n",
        "           # No chrY in females and one copy in males\n",
        "           { from=>1, to=>59_373_566, M=>1, F=>0 },\n",
        "       ],\n",
        "       MT =>\n",
        "       [\n",
        "           # Haploid MT in males and females\n",
        "           { from=>1, to => 16_569, M=>1, F=>1 },\n",
        "       ],\n",
        "   }\n",
        "\n";
    exit -1;
}


sub parse_params
{
    my $opts = 
    {
        ploidy =>
        {
            X =>
            [
                { from=>1, to=>60_000, M=>1 },
                { from=>2_699_521, to=>154_931_043, M=>1 },
            ],
            Y =>
            [
                { from=>1, to=>59_373_566, M=>1, F=>0 },
            ],
            MT =>
            [
                { from=>1, to => 16_569, M=>1, F=>1 },
            ],
        },
    };
    while (defined(my $arg=shift(@ARGV)))
    {
        if ( $arg eq '-p' || $arg eq '--ploidy' ) { my $file=shift(@ARGV); my $x=do $file; $$opts{ploidy}=$x; next }
        if ( $arg eq '-s' || $arg eq '--samples' ) { $$opts{samples}=shift(@ARGV); next }
        if ( $arg eq '-a' || $arg eq '--assumed-sex' ) { $$opts{assumed_sex}=shift(@ARGV); next }
        if ( $arg eq '-l' || $arg eq '--fix-likelihoods' ) { $$opts{fix_likelihoods}=1; next }
        if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
        error("Unknown parameter \"$arg\". Run -h for help.\n");
    }
    if ( !exists($$opts{samples}) ) { error("Missing the -s option.\n") }
    return $opts;
}

sub fix_ploidy
{
    my ($opts) = @_;
    my $vcf = $$opts{vcf} = Vcf->new(fh=>\*STDIN);
    $vcf->parse_header();
    init_regions($opts);
    print $vcf->format_header;

    my @samples = $vcf->get_samples;
    my ($prev_chr,$prev_pos,$regions,$iregion,$nregions);
    my %nchanged;
    while (my $line = $vcf->next_line)
    {
        my $rec = $vcf->next_data_array($line);
        if ( !defined $prev_chr or $$rec[0] ne $prev_chr )
        {
            $prev_chr = $$rec[0];
            $prev_pos = $$rec[1];
            if ( exists($$opts{regions}{$prev_chr}) )
            {
                $regions  = $$opts{regions}{$prev_chr};
                $iregion  = 0;
                $nregions = @$regions;
            }
            else
            {
                $regions = undef;
            }
        }
        $prev_chr = $$rec[0];
        $prev_pos = $$rec[1];

        my $samples;
        if ( defined $regions )
        {
            if ( $prev_pos >= $$regions[$iregion]{from} && $prev_pos <= $$regions[$iregion]{to} )
            {
                $samples = $$regions[$iregion]{samples};
            }
            else
            {
                while ( $iregion<$nregions && $$regions[$iregion]{to}<$prev_pos ) { $iregion++; }
                if ( $iregion>=$nregions ) { undef $regions; }
                elsif ( $prev_pos >= $$regions[$iregion]{from} && $prev_pos <= $$regions[$iregion]{to} )
                {
                    $samples = $$regions[$iregion]{samples};
                }
            }
        }

        if ( !defined $samples ) { print $line; next; }

        my $igt = $vcf->get_tag_index($$rec[8],'GT',':');
        my $ipl = $vcf->get_tag_index($$rec[8],'PL',':');
        my $igl = $vcf->get_tag_index($$rec[8],'GL',':');
        if ( $igt==-1 ) { print $line; next; }

        my @alt = split(/,/,$$rec[4]);
        my $nals = $alt[0] eq '.' ? 1 : 1 + scalar @alt;

        my $changed = 0;
        my $nrec = @$rec;
        for (my $isample=9; $isample<$nrec; $isample++)
        {
            my $sample = $samples[$isample-9];
            if ( !exists($$samples{$sample}) ) { next; }

            my $gt = $vcf->get_field($$rec[$isample],$igt);
            my ($pl,$gl);
            if ( $$opts{fix_likelihoods} && $ipl != -1 ) { $pl = $vcf->get_field($$rec[$isample],$ipl); }
            if ( $$opts{fix_likelihoods} && $igl != -1 ) { $gl = $vcf->get_field($$rec[$isample],$igl); }
            
            my ($new_gt, $new_pl, $new_gl);
            if ( !$$samples{$sample} )
            {
                # missing genotype - leave it as it is unless it must be removed
                if ( $gt ne '.' && $gt ne './.' ) 
                { 
                    my (@als) = $vcf->split_gt($gt);
                    if ( defined $pl && $pl ne '.' ) { ($new_pl) = reploid_g($rec, 1,  $nals, $pl, scalar @als, 1); }
                    if ( defined $gl && $gl ne '.' ) { ($new_gl) = reploid_g($rec, -1, $nals, $gl, scalar @als, 1); }
                    $new_gt = '.'; 
                    $nchanged{removed}{$sample}++; 
                }
            }
            else
            {
                my (@als) = $vcf->split_gt($gt);
                if ( $$samples{$sample} != @als )
                {
                    $new_gt = join('/',($als[0]) x $$samples{$sample});
                    if ( defined $pl && $pl ne '.' ) { ($new_pl,$new_gt) = reploid_g($rec, 1,  $nals, $pl, scalar @als, $$samples{$sample}); }
                    if ( defined $gl && $gl ne '.' ) { ($new_gl,$new_gt) = reploid_g($rec, -1, $nals, $gl, scalar @als, $$samples{$sample}); }
                }
            }
            if ( defined $new_gt )
            {
                $$rec[$isample] = $vcf->replace_field($$rec[$isample],$new_gt,$igt,':');
                $changed++;
            }
            if ( defined $new_pl )
            {
                $$rec[$isample] = $vcf->replace_field($$rec[$isample],$new_pl,$ipl,':');
                $changed++;
            }
            if ( defined $new_gl )
            {
                $$rec[$isample] = $vcf->replace_field($$rec[$isample],$new_gl,$igl,':');
                $changed++;
            }
        }
        if ( $changed ) { print join("\t",@$rec),"\n"; }
        else { print $line; }
    }

    # Output stats
    for my $key (sort keys %nchanged)
    {
        for my $sample (sort keys %{$nchanged{$key}})
        {
            print STDERR "$sample\t$$opts{samples}{$sample}\t$key\t$nchanged{$key}{$sample}\n";
        }
    }
}

sub reploid_g
{
    my ($rec, $extr,$nals,$str,$n,$m) = @_;
    my @vals = split(/,/,$str);
    if ( $n==2 && $m==1 )
    {
        my @out;
        my $d = 1;
        my $k = 0;
        my ($imin,$min);
        for (my $i=0; $i<$nals; $i++)
        {
            if ( $k>=@vals ) { error("Cannot reploid $$rec[0]:$$rec[1], too few values in $str: $nals, $n->$m ($i,$d,$k)\n"); }
            if ( $vals[$k] ne '.' && (!defined $min or $min>$extr*$vals[$k]) )
            {
                $min = $extr*$vals[$k];
                $imin = $i;
            }
            push @out, $vals[$k];
            $d++;
            $k += $d;
        }
        my $gt = defined $imin ? $imin : 0;
        return (join(',',@out), $gt);
    }
    elsif ( $n==1 && $m==2 ) 
    {
        my @out;
        my ($imin,$min);
        for (my $i=0; $i<$nals; $i++)
        {
            for (my $j=0; $j<=$i; $j++)
            {
                push @out, $i==$j ? $vals[$i] : '.';
                if ( $vals[$i] ne '.' && (!defined $min or $min>$extr*$vals[$i]) )
                {
                     $min = $extr*$vals[$i];
                     $imin = $i;
                }
            }
        }
        my $gt = defined $imin ? $imin : 0;
        return (join(',',@out), "$gt/$gt" );
    }
    else { error("Only diploid/haploid cases handled in this version, sorry."); }
}

sub init_regions
{
    my ($opts) = @_;

    open(my $fh,'<',$$opts{samples}) or error("$$opts{samples}: $!");
    my (%sexes,%samples);
    while (my $line=<$fh>)
    {
        $line =~ s/^\s*//;
        $line =~ s/\s*$//;
        if ( !($line=~/^(\S+)\s+(\S+)$/) ) { error("Could not parse the sample file $$opts{sample}, the offending line was: $line"); }
        push @{$sexes{$2}}, $1;
        $samples{$1} = $2;
    }
    close($fh);
    $$opts{samples} = \%samples;

    for my $sample ($$opts{vcf}->get_samples())
    {
        if ( !exists($samples{$sample}) )
        {
            if ( !exists($$opts{assumed_sex}) ) { error("Could not determine the sex of the sample \"$sample\". Would the -a option help here?\n"); }
            $samples{$sample} = $$opts{assumed_sex};
            push @{$sexes{$$opts{assumed_sex}}}, $sample;
        }
    }

    # Create a quick look-up structure
    for my $chr (keys %{$$opts{ploidy}})
    {
        if ( ref($$opts{ploidy}{$chr}) ne 'ARRAY' ) { error("Uh, expected list reference for $chr regions.\n"); }

        my $prev;
        for my $reg (sort { $$a{from}<=>$$b{to} } @{$$opts{ploidy}{$chr}})
        {
            my $from = $$reg{from};
            my $to   = $$reg{to}; 

            if ( defined $prev && $prev>=$from ) { error("FIXME: Overlapping regions $chr:$prev>=$from\n"); }
            $prev = $to;
            
            my $region;
            for my $sex (keys %sexes)
            {
                if ( !exists($$reg{$sex}) ) { next; }
                for my $sample (@{$sexes{$sex}})
                {
                    $$region{samples}{$sample} = $$reg{$sex};
                }
            }
            if ( !defined $region ) { next; }
            $$region{from} = $from;
            $$region{to}   = $to;
            push @{$$opts{regions}{$chr}}, $region;
        }
    }
}