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AmpliconSearch finds amplicons in reverse-complement now
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fangly committed Mar 4, 2012
1 parent 6ff387d commit baf0917
Showing 1 changed file with 29 additions and 1 deletion.
30 changes: 29 additions & 1 deletion t/Tools/AmpliconSearch.t
Expand Up @@ -2,7 +2,7 @@ BEGIN {
use lib '.';
use Bio::Root::Test;

test_begin(-tests => 44);
test_begin(-tests => 57);

use_ok 'Bio::Tools::AmpliconSearch';
use_ok 'Bio::PrimarySeq';
Expand Down Expand Up @@ -109,6 +109,34 @@ is $amplicon->seq->seq, 'CCCCCaaaaaTTTTT';

# Amplicon on reverse strand

$seq = Bio::PrimarySeq->new(
# Reverse-complement of previous sequence... should have same amplicons
-seq => 'ttttttttttAAAAAtttttGGGGGtttttAAAAAttttttttttGGGGGttttt',
);
$forward = Bio::PrimarySeq->new(
-seq => 'CCCCC',
);
$reverse = Bio::PrimarySeq->new(
-seq => 'AAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
-template => $seq,
-forward_primer => $forward,
-reverse_primer => $reverse,
);
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 31;
is $amplicon->end, 50;
is $amplicon->strand, -1;
is $amplicon->seq->seq, 'CCCCCaaaaaaaaaaTTTTT';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 11;
is $amplicon->end, 25;
is $amplicon->strand, -1;
is $amplicon->seq->seq, 'CCCCCaaaaaTTTTT';


# Multiple amplicons on muliple strands

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