<![CDATA[
#!perl -w
use strict;
=head1 NAME
BioLibeg.pm - sample library
=head1 DESCRIPTION
A small testable function library.
=head1 SYNOPSIS
To use this module, add the line:
use BioLibeg;
Making sure the module is in the same directory
or another place where Perl can find it.
=head1 USAGE
use BioLibeg qw/codon2aa count/;
or
use BioLibeg 0.001 qw/:all/;
my $dna = "ATAGCATAG";
my $len = length $dna;
my $protein = "";
for (my $index=0; $index<$len-2; $index=+3) {
$protein .= codon2aa(substr($dna,$index,3);
}
print "DNA 2 PROTEIN: $dna => $protein\n";
my $count = count("t",$dna);
print "Count of Ts: $count\n";
=head1 BUGS
=head1 AUTHOR
David Scott E<lt>leapingfrog@yahoo.comE<gt>
=head1 Functions
Functions follow in alphabetic order.
=over 4
=cut
package BioLibeg;
use feature qw/switch/;
BEGIN {
use Exporter( );
our ($VERSION, @ISA, @EXPORT, @EXPORT_OK, %EXPORT_TAGS);
$VERSION = "0.001";
$VERSION = eval $VERSION;
@ISA = qw/Exporter/;
@EXPORT = ( );
%EXPORT_TAGS = (
all => [ qw/codon2aa count/ ],
);
@EXPORT_OK = qw/codon2aa count/;
}
# functions needing a %genetic_code hash
{
my %genetic_code = (
'TCA' => 'S', 'TCC' => 'S', 'TCG' => 'S',
'TCT' => 'S', # Serine
'TTC' => 'F', 'TTT' => 'F', # Phenylalanine
'TTA' => 'L', 'TTG' => 'L', # Leucine
'TAC' => 'Y', 'TAT' => 'Y', # Tyrosine
'TAA' => '_', 'TAG' => '_', # Stop
'TGC' => 'C', 'TGT' => 'C', # Cysteine
'TGA' => '_', # Stop
'TGG' => 'W', # Tryptophan
'CTA' => 'L', 'CTC' => 'L', 'CTG' => 'L',
'CTT' => 'L', # Leucine
'CCA' => 'P', 'CCC' => 'P', 'CCG' => 'P',
'CCT' => 'P', # Proline
'CAC' => 'H', 'CAT' => 'H', # Histidine
'CAA' => 'Q', 'CAG' => 'Q', # Glutamine
'CGA' => 'R', 'CGC' => 'R', 'CGG' => 'R',
'CGT' => 'R', # Arginine
'ATA' => 'I', 'ATC' => 'I',
'ATT' => 'I', # Isoleucine
'ATG' => 'M', # Methionine
'ACA' => 'T', 'ACC' => 'T', 'ACG' => 'T',
'ACT' => 'T', # Threonine
'AAC' => 'N', 'AAT' => 'N', # Asparagine
'AAA' => 'K', 'AAG' => 'K', # Lysine
'AGC' => 'S', 'AGT' => 'S', # Serine
'AGA' => 'R', 'AGG' => 'R', # Arginine
'GTA' => 'V', 'GTC' => 'V', 'GTG' => 'V',
'GTT' => 'V', # Valine
'GCA' => 'A', 'GCC' => 'A', 'GCG' => 'A',
'GCT' => 'A', # Alanine
'GAC' => 'D', 'GAT' => 'D', # Aspartic Acid
'GAA' => 'E', 'GAG' => 'E', # Glutamic Acid
'GGA' => 'G', 'GGC' => 'G', 'GGG' => 'G',
'GGT' => 'G', # Glycine
);
=item $amino_acid = codon2aa($codon);
Translate a DNA 3-character codon to an amino acid.
Any missing entry translates to '*'.
=cut
sub codon2aa {
my($codon) = @_;
$codon = uc $codon;
return $genetic_code{$codon} || "*";
}
}
=item $count = count($char, $dna);
Return a count of $char in the $dna string.
If it is not a dna nucleotide return -1.
=cut
sub count {
my ($char, $dna) = @_;
my $count = 0;
given ($char) {
when ( /t|T/ ) { $count = ($dna =~ tr/Tt//); }
when ( /a|A/ ) { $count = ($dna =~ tr/Aa//); }
when ( /g|G/ ) { $count = ($dna =~ tr/Gg//); }
when ( /c|C/ ) { $count = ($dna =~ tr/Cc//); }
default { $count = -1; }
}
return $count;
}
1;
__END__
]]>