#!/usr/bin/perl

use autodie;  # Automatic errors on file problems.
use strict;

# This is the name of the file we want to modify.
my $filename = 'modify-file.txt';

# We're going to create a temporary file. This avoids us having
# to build up a potentially large string in memory.
my $tempname = $filename . '.tmp';

do
{
	# Open both files. Doing this using lexical file handles
	# within a "do" block means that when the end of the block
	# is reached, the files will be closed.
	open my $input_h, '<', $filename;   # input handle
	open my $output_h, '>', $tempname;  # output handle

	# Loop through each line of input.
	while (<$input_h>)
	{
		# Modify the line
		s/^>Sample_(\d+)_x(\d+)/>ID$1 $2/i;
		
		# Write it out.
		print $output_h $_;
	}
};

# Delete the original file.
unlink $filename while -f $filename;

# Rename the temporary file to the original filename.
rename $tempname => $filename;