#!/usr/bin/perl
use strict;
use warnings;
my @params = ();
while ( my $param = shift ) {
	push @params, $param;
}
unless ( scalar @params == 4 ) {
	print "$0 <input fasta file> <block size> <block label> <output file>\n";
	exit;
}
my ( $inputFile, $blockSize, $blockLabel, $outputFile ) = @params;
print "Input seems to be valid. Now I will try reading the contents of $inputFile...";
open INPUT, '<', $inputFile or die $!;
open OUTPUT, '>', $outputFile or die $!;
my $sequence = '';
while ( <INPUT> ) {
	chomp;
	next if ( /^\s*$/ );
	next if ( /^>/ );
	$sequence .= $_;
}
print "done.\n";
my $pos = 0;
my $index = 0;
print "The sequence has ", length($sequence), " bases. Now I will try breaking it into segments, each of size $blockSize bases.\n";
while ( $pos < length($sequence) ) {
	$index++;
	print OUTPUT ">$blockLabel$index\n";
	print OUTPUT substr($sequence, $pos, $blockSize) . "\n";
	$pos += $blockSize;
}
close OUTPUT;
close INPUT;
print "Successfully generated $outputFile.\n";