#!/usr/bin/perl

use strict;
#use warnings;
use BeginPerlBioinfo;

srand ($$|time);
my $contig;
# This program will download the sequences from a given organism
my $organism;
print "Give the organism from where you want to download the sequences:\n";
$organism = <STDIN>;
chomp $organism;

#print "Give number of sequences to be generated";
#print "\n";
my $number = 10;
#chomp $number;

my @numbers = (1 .. $number);
foreach my $numbers(@numbers){
	if ($organism eq 'Homo Sapien'){
		my @chromosomes = qw\1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 'X' 'Y'\;
		# pick a random chromosome from the chromosomes in humans
		my $chromosome = random_element(@chromosomes);
		#my $contig;
		print "Chromosome $chromosome\n";	
		# pick up a contig randomly from the number of contigs present in each given chromosome
		# This is one more loop
		if ( my $chomosome eq '1'){
			my @contigs = (1 .. 30);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '2'){
			my @contigs = (1 .. 28);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq  '3'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '4'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '5'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '6'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '7'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '8'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '9'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '10'){
                	my @contigs = (1 .. 25);
                	my $contig = random_element(@contigs);
		} elsif ($chromosome eq '11'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '12'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '13'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '14'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '15'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '16'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '17'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '18'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '19'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '20'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '21'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq '22'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		} elsif ($chromosome eq 'X'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs)
		} elsif ($chromosome eq 'Y'){
			my @contigs = (1 .. 25);
			my $contig = random_element(@contigs);
		}
		
		print " Contig $contig \n";

	}
}


################
#
##############

# random_element
#
# Sub routine thta picks up random element from a given array

sub random_element{
	my @array = @_;
	return $array [rand @array];
}