#!/usr/local/bin/perl -w 
#use strict;

#####Point these paths to original cel files and an empty new folder
$oripath = "r://cel file anonymization//original cel files//";
$anonpath = "r://cel file anonymization//anonymized cel files//";

#####read in the link file; store it in array and close the file
open(linkfile,"r://B27 cel file anonymization//B27anonymizationlinkfile.txt")
	or die ("CAnt open link file!\n");
@link=<linkfile>;
shift(@link);
close(linkfile);

#####loop through the cel files, replacing the names and creating new anonymized cels
foreach $sample (@link)	{
	chomp($sample);
	($infile,$labno,$out,$anonno)=split(/\t/,$sample);
	print("Anonymizing $infile\n");
	
	
	open (INFILE, $oripath.$infile) or die "can't open file $oripath $infile $!"
	;
	binmode (INFILE);
	
	open OUTPUTFILE, ">", $anonpath.$out or die "cant open outputfile";
	
	while(<INFILE>)
		{
		$_=~s?B27-\d\d\d|B27-\d\d|B27-\d?B27-$anonno?g;
		print OUTPUTFILE $_;
		}

close (INFILE);
close (OUTPUTFILE);
}