/usr/bin/vcf-consensus is in vcftools 0.1.12+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Vcf;
my $opts = parse_params();
do_consensus($opts);
exit;
#--------------------------------
sub error
{
my (@msg) = @_;
if ( scalar @msg )
{
croak @msg;
}
die
"Usage: cat ref.fa | vcf-consensus [OPTIONS] in.vcf.gz > out.fa\n",
"Options:\n",
" -h, -?, --help This help message.\n",
" -H, --haplotype <int> Apply only variants for the given haplotype (1,2)\n",
" -s, --sample <name> If not given, all variants are applied\n",
"Examples:\n",
" # Get the consensus for one region. The fasta header lines are then expected\n",
" # in the form \">chr:from-to\".\n",
" samtools faidx ref.fa 8:11870-11890 | vcf-consensus in.vcf.gz > out.fa\n",
"\n";
}
sub parse_params
{
my $opts = { };
while (my $arg=shift(@ARGV))
{
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
if ( $arg eq '-s' || $arg eq '--sample' ) { $$opts{sample}=shift(@ARGV); next; }
if ( $arg eq '-H' || $arg eq '--haplotype' ) { $$opts{haplotype}=shift(@ARGV); next; }
if ( -e $arg && !exists($$opts{vcf_file}) ) { $$opts{vcf_file}=$arg; next; }
error("Unknown parameter \"$arg\". Run -h for help.\n");
}
if ( exists($$opts{haplotype}) && !exists($$opts{sample}) ) { error("Expected -s option with -H.\n"); }
return $opts;
}
sub do_consensus
{
my ($opts) = @_;
my $vcf = Vcf->new(file=>$$opts{vcf_file});
$vcf->parse_header;
if ( exists($$opts{sample}) )
{
if ( !exists($$vcf{has_column}{$$opts{sample}}) ) { error("No such sample: $$opts{sample}"); }
$$opts{vcf} = $vcf;
$$opts{sample_col} = $$vcf{has_column}{$$opts{sample}};
}
my $chrs = $vcf->get_chromosomes();
my %chrs = map { $_=>0 } @$chrs;
my ($chr,$vcf_pos,$warned,$vcf_line);
while (my $line=<STDIN>)
{
if ( $line=~/^>([^:\s]+)/ )
{
flush_fa_buffer($opts,0);
$chr = $1;
my $rest = $';
$$opts{fa_pos} = ($rest=~/^:(\d+)-\d+$/) ? $1 : 1;
$$opts{fa_idx} = 0;
$$opts{fa_frz} = 0;
if ( exists($chrs{$chr}) ) { $chrs{$chr}=1; }
my $region = $$opts{fa_pos} > 1 ? "$chr:$$opts{fa_pos}" : $chr;
$vcf->open(region=>$region);
print $line;
next;
}
chomp($line);
if ( !$$opts{case_known} )
{
if ( uc($line) eq $line ) { $$opts{case_known} = 'u'; }
elsif ( lc($line) eq $line ) { $$opts{case_known} = 'l'; }
else { $$opts{case_known} = 'u'; }
}
$$opts{fa_buf} .= $line;
$$opts{fa_len} += length($line);
while ( defined($vcf_line = $vcf->next_data_array()) )
{
# can the beginning of the buffer be printed?
if ( $$opts{fa_pos}+$$opts{fa_len}-$$opts{fa_idx}<=$$vcf_line[1] )
{
$vcf->_unread_line($vcf_line);
flush_fa_buffer($opts,60);
last;
}
# is the buffer long enough?
if ( $$opts{fa_pos}+$$opts{fa_len}-$$opts{fa_idx}<=$$vcf_line[1]+length($$vcf_line[3]) )
{
$vcf->_unread_line($vcf_line);
last;
}
apply_variant($opts,$vcf_line);
}
if ( !defined $vcf_line ) { flush_fa_buffer($opts,60); }
}
flush_fa_buffer($opts,0);
for my $chr (keys %chrs)
{
if ( !$chrs{$chr} ) { warn("The sequence \"$chr\" not found in the fasta file.\n"); }
}
}
sub flush_fa_buffer
{
my ($opts,$len) = @_;
while ( $$opts{fa_len} && $$opts{fa_len}>=60 )
{
print substr($$opts{fa_buf},0,60,''), "\n";
$$opts{fa_len} -= 60;
$$opts{fa_pos} += 60 - $$opts{fa_idx};
$$opts{fa_idx} = 0;
}
if ( $len or !$$opts{fa_len} ) { return; }
print $$opts{fa_buf},"\n";
$$opts{fa_pos} += $$opts{fa_len}-$$opts{fa_idx};
$$opts{fa_len} = 0;
$$opts{fa_buf} = '';
$$opts{fa_idx} = 0;
}
sub apply_variant
{
my ($opts,$vline) = @_;
if ( $$vline[4] eq '.' ) { return; }
my $hap = exists($$opts{haplotype}) ? $$opts{haplotype} : 0;
my $alt;
if ( !exists($$opts{sample_col}) )
{
my $idx;
$alt = ($idx=index($$vline[4],','))==-1 ? $$vline[4] : substr($$vline[4],0,$idx);
}
else
{
my $igt = $$opts{vcf}->get_tag_index($$vline[8],'GT',':');
if ( $igt==-1 ) { return; }
my $gt = $$opts{vcf}->get_field($$vline[$$opts{sample_col}-1],$igt);
my @als = $$opts{vcf}->split_gt($gt);
if ( $hap )
{
# Note: we are not checking the phase or phase blocks, assuming the VCF is perfect
if ( $hap <= @als && $als[$hap-1] ne '0' )
{
$alt = $$opts{vcf}->get_field($$vline[4],$als[$hap-1]-1,',');
}
}
else
{
for my $al (@als)
{
if ( $al eq '0' ) { next; }
$alt = $$opts{vcf}->get_field($$vline[4],$al-1,',');
last;
}
}
if ( !defined $alt ) { return; }
}
if ( $$vline[1] <= $$opts{fa_frz} )
{
print STDERR "Note: Conflicting variants at (or near) $$vline[0]:$$vline[1], cannot apply both.\n";
return;
}
my $pos = $$vline[1] - $$opts{fa_pos} + $$opts{fa_idx};
if ( $pos<0 or $pos>=$$opts{fa_len} ) { error("FIXME: $$vline[0]:$$vline[1] .. $$opts{fa_pos},$pos,$$opts{fa_len},$$opts{fa_frz}\n"); }
# Sanity check
my $ref_len = length($$vline[3]);
if ( $$vline[3] ne uc(substr($$opts{fa_buf},$pos,$ref_len)) )
{
error(sprintf "The fasta sequence does not match the REF at $$vline[0]:$$vline[1]. %s(%s) in .fa, %s in .vcf, frz=%d\n",
substr($$opts{fa_buf},$pos,$ref_len),
substr($$opts{fa_buf},$pos+1,$ref_len+5),
$$vline[3], $$opts{fa_frz}?$$opts{fa_frz}:0);
}
if ( $$opts{case_known} eq 'l' ) { $alt = lc($alt); }
my $alt_len = length($alt);
substr($$opts{fa_buf},$pos,$ref_len,$alt);
$$opts{fa_len} += $alt_len - $ref_len;
$$opts{fa_pos} += $ref_len; # position with respect to the original reference sequence
$$opts{fa_idx} += $alt_len; # position in the modified sequence
$$opts{fa_frz} = $$vline[1] + $ref_len - 1; # freeze changes until this position
}
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