--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/unix_tools/find_and_replace.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,202 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Std;
+
+sub parse_command_line();
+sub build_regex_string();
+sub usage();
+
+my $input_file ;
+my $output_file;
+my $find_pattern ;
+my $replace_pattern ;
+my $find_complete_words ;
+my $find_pattern_is_regex ;
+my $find_in_specific_column ;
+my $find_case_insensitive ;
+my $replace_global ;
+my $skip_first_line ;
+
+
+##
+## Program Start
+##
+usage() if @ARGV<2;
+parse_command_line();
+my $regex_string = build_regex_string() ;
+
+# Allow first line to pass without filtering?
+if ( $skip_first_line ) {
+	my $line = <$input_file>;
+	print $output_file $line ;
+}
+
+
+##
+## Main loop
+##
+
+## I LOVE PERL (and hate it, at the same time...)
+##
+## So what's going on with the self-compiling perl code?
+##
+## 1. The program gets the find-pattern and the replace-pattern from the user (as strings).
+## 2. If both the find-pattern and replace-pattern are simple strings (not regex), 
+##    it would be possible to pre-compile a regex (with qr//) and use it in a 's///'
+## 3. If the find-pattern is a regex but the replace-pattern is a simple text string (with out back-references)
+##    it is still possible to pre-compile the regex and use it in a 's///'
+## However,
+## 4. If the replace-pattern contains back-references, pre-compiling is not possible.
+##    (in perl, you can't precompile a substitute regex).
+##    See these examples:
+##    http://www.perlmonks.org/?node_id=84420
+##    http://stackoverflow.com/questions/125171/passing-a-regex-substitution-as-a-variable-in-perl
+##
+##    The solution:
+##    we build the regex string as valid perl code (in 'build_regex()', stored in $regex_string ),
+##    Then eval() a new perl code that contains the substitution regex as inlined code.
+##    Gotta love perl!
+
+my $perl_program ;
+if ( $find_in_specific_column ) {
+	# Find & replace in specific column
+
+	$perl_program = <<EOF;
+	while ( <STDIN> ) {
+		chomp ;
+		my \@columns = split ;
+
+		#not enough columns in this line - skip it
+		next if ( \@columns < $find_in_specific_column ) ;
+
+		\$columns [ $find_in_specific_column - 1 ] =~ $regex_string ;
+
+		print STDOUT join("\t", \@columns), "\n" ;
+	}
+EOF
+
+} else {
+	# Find & replace the entire line
+	$perl_program = <<EOF;
+		while ( <STDIN> ) {
+			$regex_string ;
+			print STDOUT;
+		}
+EOF
+}
+
+
+# The dynamic perl code reads from STDIN and writes to STDOUT,
+# so connect these handles (if the user didn't specifiy input / output
+# file names, these might be already be STDIN/OUT, so the whole could be a no-op).
+*STDIN = $input_file ;
+*STDOUT = $output_file ;
+eval $perl_program ;
+
+
+##
+## Program end
+##
+
+
+sub parse_command_line()
+{
+	my %opts ;
+	getopts('grsiwc:o:', \%opts) or die "$0: Invalid option specified\n";
+
+	die "$0: missing Find-Pattern argument\n" if (@ARGV==0); 
+	$find_pattern = $ARGV[0];
+	die "$0: missing Replace-Pattern argument\n" if (@ARGV==1); 
+	$replace_pattern = $ARGV[1];
+
+	$find_complete_words = ( exists $opts{w} ) ;
+	$find_case_insensitive = ( exists $opts{i} ) ;
+	$skip_first_line = ( exists $opts{s} ) ;
+	$find_pattern_is_regex = ( exists $opts{r} ) ;
+	$replace_global = ( exists $opts{g} ) ;
+
+	# Search in specific column ?
+	if ( defined $opts{c} ) {
+		$find_in_specific_column = $opts{c};
+
+		die "$0: invalid column number ($find_in_specific_column).\n"
+			unless $find_in_specific_column =~ /^\d+$/ ;
+			
+		die "$0: invalid column number ($find_in_specific_column).\n"
+			if $find_in_specific_column <= 0; 
+	}
+	else {
+		$find_in_specific_column = 0 ;
+	}
+
+	# Output File specified (instead of STDOUT) ?
+	if ( defined $opts{o} ) {
+		my $filename = $opts{o};
+		open $output_file, ">$filename" or die "$0: Failed to create output file '$filename': $!\n" ;
+	} else {
+		$output_file = *STDOUT ;
+	}
+
+
+	# Input file Specified (instead of STDIN) ?
+	if ( @ARGV>2 ) {
+		my $filename = $ARGV[2];
+		open $input_file, "<$filename" or die "$0: Failed to open input file '$filename': $!\n" ;
+	} else {
+		$input_file = *STDIN;
+	}
+}
+
+sub build_regex_string()
+{
+	my $find_string ;
+	my $replace_string ;
+
+	if ( $find_pattern_is_regex ) {
+		$find_string = $find_pattern ;
+		$replace_string = $replace_pattern ;
+	} else {
+		$find_string = quotemeta $find_pattern ;
+		$replace_string = quotemeta $replace_pattern;
+	}
+
+	if ( $find_complete_words ) {
+		$find_string = "\\b($find_string)\\b"; 
+	}
+
+	my $regex_string = "s/$find_string/$replace_string/";
+
+	$regex_string .= "i" if ( $find_case_insensitive );
+	$regex_string .= "g" if ( $replace_global ) ;
+	
+
+	return $regex_string;
+}
+
+sub usage()
+{
+print <<EOF;
+
+Find and Replace
+Copyright (C) 2009 - by A. Gordon ( gordon at cshl dot edu )
+
+Usage: $0 [-o OUTPUT] [-g] [-r] [-w] [-i] [-c N] [-l] FIND-PATTERN REPLACE-PATTERN [INPUT-FILE]
+
+   -g   - Global replace - replace all occurences in line/column. 
+          Default - replace just the first instance.
+   -w   - search for complete words (not partial sub-strings).
+   -i   - case insensitive search.
+   -c N - check only column N, instead of entire line (line split by whitespace).
+   -l   - skip first line (don't replace anything in it)
+   -r   - FIND-PATTERN and REPLACE-PATTERN are perl regular expression,
+          usable inside a 's///' statement.
+          By default, they are used as verbatim text strings.
+   -o OUT - specify output file (default = STDOUT).
+   INPUT-FILE - (optional) read from file (default = from STDIN).
+
+
+EOF
+
+	exit;
+}