I am not a programmer by any stretch of the imagination but was recently volunteered to anonymize several thousand binary files, which involves replacing a 1,2,or 3 digit number with a different 1,2,or 3 digit number. so i thought now would be a good time to learn perl.

After some experimentation I have a script that does what I want but the output files are recognized as corrupted by the software I use to compile them. They are each about 4kb larger than original, and when I look at them in hexeditor I see original had 0a line separator and the output has 2 characters I think it was 0a 0d. I am working in win xp with strawberry; not sure what os original files were on.

After more reading I thought I could use -l012 on command line but that had the effect of adding additional blank lines, effectively double spacing the file.
thanks. Heres my code:

#!/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//B27anonymizationlinkfil
+e.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);
}
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