From 036b8f518d47f646da1328205f12dcd08acec83e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 1 Sep 2010 13:26:10 +0000
Subject: [PATCH] Utilities for processing VCF
---
bcftools/vcfutils.pl | 59 ++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 59 insertions(+)
create mode 100755 bcftools/vcfutils.pl
diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
new file mode 100755
index 0000000..bf77049
--- /dev/null
+++ b/bcftools/vcfutils.pl
@@ -0,0 +1,59 @@
+#!/usr/bin/perl -w
+
+# Author: lh3
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+&main;
+exit;
+
+sub main {
+ my $version = '0.1.0';
+ &usage if (@ARGV < 1);
+ my $command = shift(@ARGV);
+ my %func = (subsam=>\&subsam);
+ die("Unknown command \"$command\".\n") if (!defined($func{$command}));
+ &{$func{$command}};
+}
+
+sub subsam {
+ die(qq/Usage: vcfutils.pl subsam <in.vcf> [samples]\n/) if (@ARGV == 0);
+ my ($fh, %h);
+ my $fn = shift(@ARGV);
+ my @col;
+ open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
+ $h{$_} = 1 for (@ARGV);
+ while (<$fh>) {
+ if (/^##/) {
+ print;
+ } elsif (/^#/) {
+ my @t = split;
+ my @s = @t[0..8]; # all fixed fields + FORMAT
+ for (9 .. $#t) {
+ if ($h{$t[$_]}) {
+ push(@s, $t[$_]);
+ push(@col, $_);
+ }
+ }
+ pop(@s) if (@s == 9); # no sample selected; remove the FORMAT field
+ print join("\t", @s), "\n";
+ } else {
+ my @t = split;
+ if (@col == 0) {
+ print join("\t", @t[0..7]), "\n";
+ } else {
+ print join("\t", @t[0..8], map {$t[$_]} @col), "\n";
+ }
+ }
+ }
+ close($fh);
+}
+
+sub usage {
+ die(qq/
+Usage: vcfutils.pl <command> [<arguments>]\n
+Command: subsam get a subset of samples
+\n/);
+}
--
2.39.5