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#!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Bowtie 2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
#
package RandDNA;
use strict;
use Carp;
use FindBin qw($Bin);
use lib $Bin;
use DNA;
use Test;
##
# Create a new random DNA generator
#
sub new {
my (
$class,
$name, # name of generator
$n, # N fraction
$iupac, # Non-A/C/G/T/N IUPAC fraction (after N fraction removed)
$at, # AT fraction (after N/IUPAC fractions removed)
$a, # A fraction (of AT)
$c, # C fraction (of CG)
) = @_;
$name = "noname" unless defined($name);
return bless {
_name => $name,
_n => $n || croak("No N frac"),
_iupac => $iupac || croak("No IUPAC frac"),
_at => $at || rand(),
_a => $a || rand(),
_c => $c || rand()
}, $class;
}
sub name { return $_[0]->{_name} }
sub nFrac { return $_[0]->{_n} }
sub iupacFrac { return $_[0]->{_iupac} }
sub atFrac { return $_[0]->{_at} }
sub aFrac { return $_[0]->{_a} }
sub cFrac { return $_[0]->{_c} }
##
# Return a random IUPAC character.
#
sub randIUPAC() {
my @iu = (
"R",
"Y",
"M",
"K",
"S",
"W",
"B",
"V",
"H",
"D"
);
my $iui = int(rand(scalar(@iu)));
defined($iu[$iui]) || die "Bad index $iui";
return $iu[$iui];
}
##
# Given parameters controlling character frequencies, build a palette
# of short sequences that can be composed to make longer sequences.
#
sub genBuildingBlocks {
my ($self, $arr, $num, $bbrnd) = @_;
defined($arr) || die;
$num = 30 unless defined($num);
# Random generator for length
$bbrnd = sub { return int(rand(100))+1 } unless defined($bbrnd);
for my $i (1..$num) {
my $seq = "";
# Generate length
my $len = $bbrnd->();
$len > 0 || die "Bad length: $len";
# Generate characters
for my $j (1..$len) {
my $c = "";
if(rand() < $self->nFrac()) {
$c = "N";
} elsif(rand() < $self->iupacFrac()) {
$c = randIUPAC();
defined($c) || die;
} else {
$c = (rand() < $self->atFrac()) ? "AT" : "CG";
if($c eq "AT") {
$c = (rand() < $self->aFrac()) ? "A" : "T";
} else {
$c = (rand() < $self->cFrac()) ? "C" : "G";
}
}
$seq .= $c;
}
# Add to return list
push @$arr, $seq;
}
}
##
# Use this generator to generate another random sequence.
#
sub nextSeq {
my ($self, $len, $bbsr, $runrnd) = @_;
my $seq = "";
# Generate building blocks
my @bbs = ();
if(defined($bbsr)) {
@bbs = @$bbsr;
} else {
$self->genBuildingBlocks(\@bbs);
}
scalar(@bbs) > 0 || die;
# Random generator for run length
my $defaultRnd = sub {
# Mean of exp is 1/lambda
return int(Math::Random::random_exponential(1, 2))+1;
};
$runrnd = $defaultRnd unless defined($runrnd);
# Build the sequence by repeatedly inserting runs of building blocks
while(length($seq) < $len * 5) {
# Choose building block
my $bbi = int(rand(scalar(@bbs)));
# Choose how many times to add it
my $runlen = $runrnd->();
# Choose insert point
my $insat = int(rand(length($seq)));
# Repeatedly insert building lock
for my $i (1..$runlen) {
substr($seq, $insat, 0) = $bbs[$bbi];
}
}
# Return chopped out piece
return substr($seq, $len * 2, $len);
}
sub test1 {
my $rd = RandDNA->new(
"randtest1", # name
0.02, # n frac
0.01, # IUPAC frac
0.4, # AT frac
0.45, # A/AT frac
0.35); # C/CG frac
my $seq = $rd->nextSeq(200, undef);
length($seq) == 200 || die;
return 1;
}
sub test2 {
my @bb = ("AAA", "CCCC");
my $rd = RandDNA->new(
"randtest2", # name
0.02, # n frac
0.01, # IUPAC frac
0.4, # AT frac
0.45, # A/AT frac
0.35); # C/CG frac
my $seq = $rd->nextSeq(300, \@bb);
length($seq) == 300 || die;
return 1;
}
if($0 =~ /[^0-9a-zA-Z_]?RandDNA\.pm$/) {
print "Skipping unit tests requiring Math::Random which is non-free\n";
# Run unit tests
# Test::shouldSucceed("test1", \&test1);
# Test::shouldSucceed("test2", \&test2);
}
1;
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