diff bed2wig.pl @ 0:07745c0958dd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed2wig.pl	Thu Sep 18 21:40:25 2014 -0400
@@ -0,0 +1,64 @@
+#!/usr/bin/perl -w
+#Filename:
+#Author: Chentt
+#Email: [e-mail]
+#Date: 2014/06/25
+#Modified:
+#Description: get out larger than cut off sequence
+my $version=1.00;
+
+use strict;
+use Getopt::Long;
+use File::Basename;
+use FileHandle;
+
+my %opts;
+GetOptions(\%opts,"i=s","o=s","h");
+if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
+&usage;
+}
+
+my $outputdir=$opts{'o'};
+unless ($outputdir=~/\/$/) {$outputdir .="/";}
+
+##############################get cmap################## 
+my %cmap;
+open IN,"<$opts{i}";
+while (my $aline=<IN>) {
+	chomp $aline;
+	next if($aline=~/^\#/);
+	my @temp=split/\t/,$aline;
+	$cmap{$temp[0]}=$outputdir.$temp[0];
+}
+close IN;
+###########################split ma file######################
+my %handle;
+foreach  (keys %cmap) {
+	my $name=$cmap{$_}.".sam";
+	open $handle{$_},">$name";
+}
+open IN,"<$opts{i}";
+while (my $aline=<IN>) {
+	next if($aline=~/^\#/);
+	chomp $aline;
+	my @temp=split/\t/,$aline;
+	$handle{$temp[0]}-> print ($aline,"\n");
+	
+}
+close IN;
+foreach  (keys %handle) {close $_;}
+
+
+sub usage{
+print <<"USAGE";
+Version $version
+Usage:
+$0 -i -o
+options:
+-i input file
+-o output file
+-h help
+USAGE
+exit(1);
+}
+