Fixed generate_random_sequence() at sequence_oop_example.pl
Furthermore, messages appeared during git commit

1. generate_random_sequence() at sequence_oop_example.pl
Original:
my $DNA = Sequence_OOP::Sequence::generate_random_sequence(10000 ...etc)
Fixed:
my $DNA = generate_random_sequence(100000 ...etc)

2. These messages (not exact) also generated during git commit:
"CRLF is changed to LF" on ../sequences/E.coli.fasta.gz
"CRLF is changed to LF" on ../sequences/sequences.fa.gz
"CRLF is changed to LF" on ../sequences/sequences.gbk.gz
Fixed generate_kmer_sequence() at sequence_oop_example.pl

1. generate_kmer_sequence()
Original:
my %kmer = %{Sequence_OOP::Sequence::count_kmer(3, $DNA->{sequence})};
$DNA = Sequence_OOP::generate_kmer_sequence(100000, \%kmer);
Modified:
my %kmer = ("AAA" => 2, "ATT" => 2, "TAA" => 2);
$DNA = generate_kmer_sequence(100000, \%kmer);
Fixed translate() at sequence_oop_example.pl
Original:
my $Translate = Sequence_OOP::Seqeunce::translate($DNA);
Modified:
my $Translate = $DNA->translate;
Removed my non-OOP count_kmer() at Sequence_OOP.pm
Minor fix at translate() at Sequence_OOP.pm

Original:
if (undef $self->{seq_type} ...)
Modified:
if (not defined($self->{seq_type}) ...)
Fixed bug at generate_random_sequence() at Sequence_OOP.pm

Original:
my $new_obj = new Sequence("Randomized_seq", $random_seq, $seq_type);
Modified:
my $new_obj = new Sequence($random_seq, "random_seq", $seq_type);

Order of output was wrong because new object should be:
my $new_seq = (sequence, header, seq_type)
(see sub new at package Sequence at Sequence_OOP.pm)
Fixed generate_kmer_sequence() at Sequence_OOP.pm
Original:
my $new_obj = new Sequence("Randomized_seq_kmer", $seq, "DNA");
Modified:
my $new_obj = new Sequence($seq, "random_kmer_seq, "DNA");

Order of output was wrong because a new sequence object should be:
my $new_seq = (sequence, header, seq_type)
(see sub new at package Sequence at Sequence_OOP.pm)
Fixed generate_random_sequence() at Sequence_OOP.pm
Missed quote at "random_kmer_seq
should be "random_kmer_seq"
Fixed generate_kmer_sequence() at Sequence_OOP.pm

Changed output structure
Original
my $new_obj = new Sequence($seq, "random_kmer_seq", "DNA");
Modified
my $new_obj = new Sequence(     SEQUENCE        => $seq,
                                HEADER          => "random_kmer_seq",
                                TYPE            => "DNA");
Fixed generate_random_sequence() at Sequence_OOP.pm

Changed output structure

Original:
my $new_obj = new Sequence($random_seq, "random_seq", $seq_type);
Modified:
my $new_obj = new Sequence(     SEQUENCE        => $random_seq,
                                HEADER          => "random_seq",
                                TYPE            => $seq_type);
Fixed translate() at Sequence_OOP.pm

"If" function that supposed to check for seq type broke because
I used or instead of and

Original:
if (not defined($self->{seq_type}) or $self->{seq_type} ne "DNA" or
Modified:
if (not defined($self->{seq_type}) and $self->{seq_type} ne "DNA" and
Changed translate() at Sequence_OOP.pm
Translate() at Sequence Package
Changed output structure

Original:
my $new_obj = new Sequence($self->{header}, $trans, "PROTEIN");
Modified:
my $new_obj = new Sequence(     SEQUENCE        => "$trans",
                                HEADER          => $self->{header},
                                TYPE            => "PRO");
Removed translate() at Sequences at Sequence_OOP.pm
Added POD for generate_random_sequence() at Sequence_OOP.pm

Added:
=head2 generate_random_sequence

Returns a random sequence of type $type and length $length.
$type (case insensitive) can be "dna" (default), "rna",
"protein", or "custom".
dna, rna, and protein will give equal
weight to each alphabet (DNA - A/T/G/C, Protein - 20 am
ino acids).
"custom" will have a third input hash reference $hash, which will have the alphabet as key an
d weight as value

Example:

my %biased_kmer = (
"A" => 0.5,
"T" => 0.3,
"G" => 0.05,
"C" => 0.15);

my $new_seq = generate_random_sequence{100000,"custom","DNA",\%biased_kmer);

=cut
Added POD for generate_kmer_sequence at Sequence_OOP.pm
Added POD for translate() at Sequence package at Sequence_OOP.pm