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# -*-Perl-*- Test Harness script for Bioperl
# $Id: RNAChange.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 31);
use_ok('Bio::Variation::Allele');
use_ok('Bio::Variation::RNAChange');
use_ok('Bio::Variation::AAChange');
}
ok my $obj = Bio::Variation::RNAChange->new();
$obj->start(4);
is $obj->start, 4;
$obj->end(4);
is $obj->end, 4;
$obj->length(1);
is $obj->length, 1;
$obj->strand('1');
is $obj->strand, '1';
is ($obj->primary_tag, 'Variation' );
$obj->source_tag('source');
is ($obj->source_tag, 'source' );
$obj->frame(2);
is ($obj->frame, 2 );
$obj->score(2);
is ($obj->score, 2 );
#test gff string
#$obj->dna_mut('dna_mut');
#if ($obj->dna_mut eq 'dna_mut' ) {
# print "ok 11\n";
#} else {
# print "not ok 11\n";
#}
my $a1 = Bio::Variation::Allele->new(-seq => 'g');
$obj->allele_ori($a1);
is( $obj->allele_ori->seq, 'g' );
my $a2 = Bio::Variation::Allele->new('-seq' => 'a');
$obj->allele_mut($a2);
is($obj->allele_mut->seq, 'a' );
$obj->upStreamSeq('gaagattcagccaagctcaaggatg');
is ($obj->upStreamSeq, 'gaagattcagccaagctcaaggatg' );
$obj->cds_end(1000);
is ($obj->cds_end, 1000 );
$obj->dnStreamSeq('aagtgcagttagggctgggaagggt');
is ($obj->dnStreamSeq, 'aagtgcagttagggctgggaagggt' );
$obj->codon_pos(1);
is ($obj->codon_pos, 1 );
my $obj3 = Bio::Variation::AAChange->new();
$obj3->start(2);
$obj->AAChange($obj3);
$obj3->allele_ori($a1);
$obj3->allele_mut($a2);
is ($obj->label, 'missense' , "label is". $obj->label);
$obj->status('proven');
is ($obj->status, 'proven' );
$obj->proof('experimental');
is ($obj->proof, 'experimental' );
is ($obj->restriction_changes, '-BccI' );
$obj->region('coding');
is ($obj->region, 'coding' );
$obj->numbering('coding');
is ($obj->numbering, 'coding' );
is ($obj->codon_ori, 'gaa', "Codon_ori is |". $obj->codon_ori. "|");
is($obj->codon_mut, 'aaa' , "Codon_mut is |". $obj->codon_mut. "|");
$obj->codon_pos(1);
is ($obj->codon_pos, 1 );
is( $obj->codon_table, 1 );
$obj->codon_table(3);
is ( $obj->codon_table, 3 );
$obj->mut_number(2);
is ( $obj->mut_number, 2 );
$obj->verbose(2);
is ( $obj->verbose, 2 );
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