#!/usr/bin/env perl

use strict;
use warnings;

my @k_vals = (71, 73, 75, 77, 79);

print '#!/bin/bash', "\n\n", ;

foreach my $k_val (@k_vals) { 
    print "    velveth Csp9_Berkeley_20apr2012_k$k_val $k_val", ' -create_binary -fasta.gz',
          ' -short unpaired2/CS004_NoIndex_L002_R12.khmer142-1.unpaired.fa.gz',
          ' -shortPaired paired2/CS004_NoIndex_L002_R12.khmer142-1.paired.fa.gz ; ', 
          "\n",
          "    program_done_e-ping.pl -p velveth_Csp9_Berkeley_20apr2012_k$k_val ; \n",
          "\n",
          "    velvetg Csp9_Berkeley_20apr2012_k$k_val -cov_cutoff auto -exp_cov auto -min_contig_lgth 200 -ins_length 335 ; \n",
          "    program_done_e-ping.pl -p velvet_assembly_Csp9_Berkeley_20apr2012_k$k_val ; \n",
          "\n",
          ;
}