oligo_design_meth.pl

#!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Long;
use Data::Dumper;
use FindBin qw($Bin $Script);
use File::Basename qw(basename dirname);
require "/data/bioit/biodata/zenghp/bin/perl_mylib/tool.lib.pl";

my $BEGIN_TIME=time();
my $version="1.0.0";
#######################################################################################

# ------------------------------------------------------------------
# GetOptions
# ------------------------------------------------------------------
my ($fseq, $fmark,$fkey,$outdir);
GetOptions(
				"help|?" =>\&USAGE,
				"is:s"=>\$fseq,
				"im:s"=>\$fmark,
				"k:s"=>\$fkey,
				"od:s"=>\$outdir,
				) or &USAGE;
&USAGE unless ($fseq and $fmark and $fkey);

$outdir||="./";
`mkdir $outdir`	unless (-d $outdir);
$outdir=AbsolutePath("dir",$outdir);

my ($min_len, $max_len, $scale_len)=split /,/, $range_len;

## get template seq containing snp
my %seq_snp;
if(defined $ftem_snp){
	open(I, $ftem_snp) or die $!;
	$/=">";
	while(<I>){
		chomp;
		next if(/^$/);
		my ($id_info, @line)=split /\n/, $_;
		my $seq = join("", @line);
		my ($id)=split /\s+/, $id_info;
		$seq_snp{$id}=$seq;
	}
}






#######################################################################################
print STDOUT "\nDone. Total elapsed time : ",time()-$BEGIN_TIME,"s\n";
#######################################################################################

# ------------------------------------------------------------------
# sub function
# ------------------------------------------------------------------

sub USAGE {#
	my $usage=<<"USAGE";
Program:
Version: $version
Contact:zeng huaping<huaping.zeng\@genetalks.com> 

Usage:
  Options:
  -i  <file>   Input file, forced
  -k  <str>	   Key of output file, forced
  -od <dir>	   Dir of output file, default ./
  -h		   Help

USAGE
	print $usage;
	exit;
}