From: Heng Li <lh3@live.co.uk>
Date: Wed, 1 Sep 2010 16:50:33 +0000 (+0000)
Subject: more commands for my own uses
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=7ef82722e41143d313b37394b905239ae61ca19a;p=samtools.git

more commands for my own uses
---

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index bf77049..0fe1af8 100755
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -13,7 +13,7 @@ sub main {
   my $version = '0.1.0';
   &usage if (@ARGV < 1);
   my $command = shift(@ARGV);
-  my %func = (subsam=>\&subsam);
+  my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats);
   die("Unknown command \"$command\".\n") if (!defined($func{$command}));
   &{$func{$command}};
 }
@@ -51,9 +51,101 @@ sub subsam {
   close($fh);
 }
 
+sub listsam {
+  die(qq/Usage: vcfutils.pl listsam <in.vcf>\n/) if (@ARGV == 0 && -t STDIN);
+  while (<>) {
+	if (/^#/ && !/^##/) {
+	  my @t = split;
+	  print join("\n", @t[9..$#t]), "\n";
+	  exit;
+	}
+  }
+}
+
+sub fillac {
+  die(qq/Usage: vcfutils.pl fillac <in.vcf>\n\nNote: The GT field MUST BE present and always appear as the first field.\n/) if (@ARGV == 0 && -t STDIN);
+  while (<>) {
+	if (/^#/) {
+	  print;
+	} else {
+	  my @t = split;
+	  my @c;
+	  my $n = 0;
+	  $c[1] = 0;
+	  for (9 .. $#t) {
+		if ($t[$_] =~ /^(\d+).(\d+)/) {
+		  ++$c[$1]; ++$c[$2];
+		  $n += 2;
+		}
+	  }
+	  my $AC = "AC=" . join("\t", @c[1..$#c]) . ";AN=$n";
+	  my $info = $t[7];
+	  $info =~ s/(;?)AC=(\d+)//;
+	  $info =~ s/(;?)AN=(\d+)//;
+	  if ($info eq '.') {
+		$info = $AC;
+	  } else {
+		$info .= ";$AC";
+	  }
+	  $t[7] = $info;
+	  print join("\t", @t), "\n";
+	}
+  }
+}
+
+sub qstats {
+  my %opts = (r=>'', s=>0.01);
+  getopts('r:s:', \%opts);
+  die("Usage: vcfutils.pl qstats [-r ref.vcf] <in.vcf>\n
+Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #joint ts/tv #joint/#ref #joint/#non-indel \n") if (@ARGV == 0 && -t STDIN);
+  my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
+  my %h = ();
+  if ($opts{r}) { # read the reference positions
+	my $fh;
+	open($fh, $opts{r}) || die;
+	while (<$fh>) {
+	  next if (/^#/);
+	  $h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
+	}
+	close($fh);
+  }
+  my $hsize = scalar(keys %h);
+  my @a;
+  while (<>) {
+	next if (/^#/);
+	my @t = split;
+	next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
+	my @s = split(',', $t[4]);
+	$t[3] = uc($t[3]); $t[4] = uc($t[4]);
+	next if (length($s[0]) != 1);
+	push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $h{$t[0],$t[1]}? 1 : 0]);
+  }
+  push(@a, [-1, 0, 0, 0]); # end marker
+  die("[qstats] No SNP data!\n") if (@a == 0);
+  @a = sort {$b->[0]<=>$a->[0]} @a;
+  my $next = $opts{s};
+  my $last = $a[0];
+  my @c = (0, 0, 0, 0);
+  for my $p (@a) {
+	if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
+	  my @x;
+	  $x[0] = sprintf("%.3f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
+	  $x[1] = sprintf("%.3f", $hsize? $c[3] / $hsize : 0);
+	  $x[2] = sprintf("%.3f", $c[3] / $c[0]);
+	  print join("\t", $last, @c, @x), "\n";
+	  $next = $c[0]/@a + $opts{s};
+	}
+	++$c[0]; $c[1] += $p->[1]; $c[2] += $p->[2]; $c[3] += $p->[3];
+	$last = $p->[0];
+  }
+}
+
 sub usage {
   die(qq/
 Usage:   vcfutils.pl <command> [<arguments>]\n
 Command: subsam       get a subset of samples
+         listsam      list the samples
+         fillac       fill the allele count field
+         qstats       SNP stats stratified by QUAL
 \n/);
 }