#!/usr/bin/perl -w
use strict;
use FileHandle;
use Data::Dumper;

open(my $in1, "/Users/mydir/Desktop/hw3_infile1.txt");
open(my $report, ">/Users/mydir/Desktop/hw3_report.txt");
my @aa_seqs = ("MPIGSKERPTFFEIFKTRCNKADLGPIS", "MDLSALRVEEVQNVINAMQKILECPIC", "MDLSAVQIQEVQNVLHAMQKILECPICLE");
my @nt_seqs = ("atgccgctaccgt", "cgcctagcgccgcatta","ccgtaggcattc", "gacctaggtcag");

#call subroutines

#pass by value $report

print $report "Values returned via pass by value:\n";
my @oligo_array = get_oligo_seqs($in1); # pass by value
print  "@oligo_array\n";
close($in1);

#print results
print  $report "Before calling subroutine:\n";
for my $aa_seqs(@aa_seqs){
	print $report "$aa_seqs\n";
}

print  $report "\n";
for my $nt_seqs(@nt_seqs){
	print $report "$nt_seqs\n";
}
print $report "\n";

#pass by reference
change_array(\@aa_seqs, \@nt_seqs);
#print results
print  $report "After calling subroutine:\n";
for my $aa_seqs(@aa_seqs){
	print $report "$aa_seqs\n";
}
print $report "\n";
for my $nt_seqs(@nt_seqs){
	print $report "$nt_seqs\n";
}
close($report);

######## Subroutines #########

sub get_oligo_seqs{
	my ($fh) = shift;
	
	while(<$fh>){
		my @fields = split /\t/;
		my $oligos = $fields[1];
		print "$oligos\n";
	}
}
	
sub change_array{
	my ($aa, $nt) = @_;
	push(@$nt, 'ggacttacgggccatataa');
	shift(@$aa);
}