#!/usr/local/bin/perl

$\ = "\n";
$, = " ";

print sum(1);
print sum(1,2,3);
print square(5,5);

# compute and return the sum of a list
sub sum {
  $sum = 0;
  # iterating through subroutine arguments 
  for (@_) {
    # $_ alias to each argument
    $sum += $_;
  }
  return $sum;
}

sub square {
    $num = @_;
    return $num**2;
}

sub makesequence {
    %args = @_;
}

$b= 0 if ! defined $b;
print make_sequence(len=>10,bp=>"at");
print make_sequence(bp=>"gcn",len=>0);

# create a random n-mer from a specified vocabulary
sub make_sequence {
  %args = @_;
  @bp = split("",$args{bp});
  $seq = "";
  for (1..$args{len}) {
    $seq .= $bp[rand(@bp)];
  }
  return $seq;
}

print urds(5);
sub urds {
  my ($n) = @_;
  @urds = ();
  for (1..$n) {
    push @urds, rand;
  }
  return @urds;
}

$seq = "atgctggg";
($x) = filter_seq($seq,"gc");
print $x;
sub filter_seq {
  ($seq,$testbp) = @_;
  @passedseq = ();  
  for (split("",$seq)) {
    push @passedseq, $_ if /[$testbp]/;
    $_ = 1;
  }
  return scalar @passedseq;
}