#!/usr/bin/perl 
use Sequence;
use strict;

my $pseq = "NVYHDGACPE VKPVDNFDWS NYHGKWWEVA KYPNSVEKYG KCGWAEYTPE GKSVKVSNYH
            VIHGKEYFIE GTAYPVGDSK IGKIYHKLTY GGVTKENVFN VLSTDNKNYI IGYYCKYDED
            KKGHQDFVWV LSRSKVLTGE AKTAVENYLI GSPVVDSQKL VYSDFSEAAC KVN";

my $nseq = "gcttgtctgt gctcgctcac tgcctgtgtg actctttgac ttttctaaga tgttacttaa    60
agagaaaaac ttgcagaata aaaacacaca ttttatattt acaatgaaag ttaatataac       120
     tcatcactca ggagttgaat agtggaagtg tataaataac ttcaaaccga ctaaggaaaa       180
     cttggggata gttgcttgat atattttttt taattaaagg aaaactcaac atcattctta       240
     gcgttatatt aatagtgttg ggaggagctg tggggccttg atacctcgag tggacacaat       300
     agtgtctggg tgacctttgt cgtggcaatt tgattattag tttcacagtt ggccccactg       360
     aagcactgat ttcaagggat gctggctgag gagagagttt cttcttgagt tccctggaag       420
     gggtccacag ttcttttctc ctacacttac gaactgaaga tgtcccctgt aaactttggc";

my $seqobj = new Sequence ( $nseq );
$seqobj->clean();
print "Cleaned seq:\n$seqobj->{seq}\n";
print "Reverse complement:\n";
print $seqobj->rc(), "\n";

print "Tidy display:\n";
print $seqobj->wrap(), "\n";

print "Translation results:\n";
print $seqobj->translate(), "\n";

print "Shuffled sequence:\n";
my $s = $seqobj->shuffle();
print "$s\n";

print "A\t\tT\t\tG\t\tC\n";
my @pcts = $seqobj->gc_content();
print "$pcts[0]\t\t$pcts[1]\t\t$pcts[2]\t\t$pcts[3]\n";

print "Shuffled sequence GC content:\n";

$seqobj = new Sequence($s);
print "A\t\tT\t\tG\t\tC\n";
@pcts = $seqobj->gc_content();
print "$pcts[0]\t\t$pcts[1]\t\t$pcts[2]\t\t$pcts[3]\n";