#!/usr/bin/perl -w

sub unwrap {
  my ($filepath) = @_;
  my $result = {};
  open(X, $filepath) || die "$!";
  local $/ = "\n>";
  while (<X>) {
    chomp;
    s/^>//;
    my @lines = split("\n");
    my $sequence_id = shift(@lines);
    my $sequence = join('', @lines);
    $result->{$sequence_id} = $sequence;

  }
  $result;
}

sub threeframes {
  my ($inhash) = @_;
  my $result = {};
  for (keys %{$inhash}) {
    my $seq = $inhash->{$_};
    $result->{$_}->{'sequence'} = $seq;
    # Do frame 1
    my @frames = $seq =~ /(...)/g;
    $result->{$_}->{'frame1'} = join(' ', @frames);
    # Do frame 2 
    $seq = substr($seq, 1);
    # Note:
    # Someone in class suggetsed
    # $seq =~ s/^.//;
    # as an alternative to the use of substr.
    # I find the s/^.// technique easier to understand.

    @frames = $seq =~ /(...)/g;
    $result->{$_}->{'frame2'} = join(' ', @frames);
    $seq = substr($seq, 1);
    @frames = $seq =~ /(...)/g;
    $result->{$_}->{'frame3'} = join(' ', @frames);
  }
  $result;
}

$x = threeframes(unwrap('/net/share/perl_refs/cosmids1.txt'));
print $x->{'ZK1307.9'}->{'frame1'}, "\n";
print $x->{'ZK1248.6'}->{'frame1'}, "\n";
print $x->{'ZK1248.6'}->{'frame3'}, "\n";