<![CDATA[
#!perl -w
use strict;
# test functions
package main;
use Test::More tests => 22;
{
BEGIN {
use_ok('Seq');
}
can_ok('Seq', qw/new read concatenate motif print
read_file/);
can_ok('RNA', qw/new/);
can_ok('DNA', qw/new count dna2rna revcom/);
# Test Seq
my $seq = Seq->new("GCAT");
isa_ok($seq, 'Seq');
isa_ok($seq, 'GetterSetter');
is($seq->seq, "GCAT", 'test $seq->seq( )');
# Test DNA
my $dna = DNA->new("GCAT");
isa_ok($dna, 'DNA');
isa_ok($dna, 'Seq');
isa_ok($dna, 'GetterSetter');
is($dna->seq, "GCAT", 'test $dna->seq( )');
# Test RNA
my $rna = RNA->new("GCAU");
isa_ok($rna, 'RNA');
isa_ok($rna, 'Seq');
isa_ok($rna, 'GetterSetter');
is($rna->seq, "GCAU", 'test $rna->seq( )');
# set up data
my $seqfile = "throwaway.data";
my $data = '
AGCTAGCTCATCATCATCATTAGBAGDADTATGAGCGCAAAAAAAA
BADBADGGGGCCCCATATATATATATATATAAAAAAAAAAAAAAAA
';
open(FILE, "> $seqfile") or die("Unable to write: $seqfile: $!");
print FILE $data;
close(FILE);
# run tests
is($seq->read_file($seqfile), 0, 'Test valid open of $seq->read_file');
$data =~ s/\s//g;
is($seq->seq, $data, 'Test valid data from $seq->read_file');
# DNA testing
my $text = $seq->dna->count();
# note the use of tab as \t and newline as \n
# These are hard to spot in testing
# I let the test tell me the answers:
# is($text,"tell me", "Test of counts and output");
is($text,"throwaway.data:\tA=45 C=12 G=11 T=17 errors=7\n",
'Test of $dna->count() and output');
my $dna1 = new DNA("AGCT");
is($dna1->revcom()->seq,"AGCT",
'Test $dna->revcom()');
# DNA 2 RNA transcription
is($dna1->dna2rna()->seq,"AGCU",'Test $dna->dna2rna()');
my $rna1 = $dna1->dna2rna;
isa_ok($rna1, 'RNA');
# Seq testing
my $seq1 = new Seq("AGCT");
is($seq1->concatenate("GATC")->seq,"AGCTGATC",
'Test $seq->concatenate()');
# Clean up any test files
unlink($seqfile) or die("Unable to delete $seqfile: $!");
# successful exit
exit (0);
}
]]>