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use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 37);
use_ok 'Bio::PrimarySeq';
use_ok 'Bio::SeqFeature::SubSeq';
}
my ($subseq, $subseq_seq, $subsubseq, $subsubseq_seq, $template);
# Basic SubSeq object
$subseq = Bio::SeqFeature::SubSeq->new();
isa_ok $subseq, 'Bio::SeqFeature::SubSeq';
isa_ok $subseq, 'Bio::SeqFeature::Generic';
is $subseq->length, undef;
# SubSeq with explicit sequence (sequence string)
ok $subseq = Bio::SeqFeature::SubSeq->new(
-seq => 'CCCCCAAAAAGGGGGTTTTT',
);
is $subseq->length, 20;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
# SubSeq with explicit sequence (sequence object)
ok $subseq = Bio::SeqFeature::SubSeq->new(
-seq => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
);
is $subseq->length, 20;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
# SubSeq with explicit sequence and coordinates
ok $subseq = Bio::SeqFeature::SubSeq->new(
-seq => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
-start => 11,
-end => 40,
-strand => -1
);
is $subseq->length, 30;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
# Subseq with implicit sequence
$template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');
ok $subseq = Bio::SeqFeature::SubSeq->new(
-start => 11,
-end => 30,
-strand => -1
);
is $subseq->length, 20;
ok $template->add_SeqFeature($subseq);
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'AAAAACCCCCTTTTTGGGGG';
# Subseq with implicit sequence
$template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');
ok $subseq = Bio::SeqFeature::SubSeq->new(
-start => 11,
-end => 30,
-strand => -1,
-template => $template,
);
is $subseq->length, 20;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'AAAAACCCCCTTTTTGGGGG';
# Sub SubSeq
ok $subsubseq = Bio::SeqFeature::SubSeq->new(
-start => 11,
-end => 15,
-strand => 1,
-template => $subseq,
);
is $subsubseq->length, 5;
ok $subsubseq_seq = $subsubseq->seq;
isa_ok $subsubseq_seq, 'Bio::PrimarySeq';
is $subsubseq_seq->seq, 'CCCCC';
# One-liner
is( Bio::SeqFeature::SubSeq->new(-start=>11,-end=>30,-strand=>1,-template=>$template)->seq->seq, 'CCCCCAAAAAGGGGGTTTTT' );
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