use
vars
qw($NUMTESTS $DEBUG $ERROR)
;
$DEBUG
=
$ENV
{
'BIOPERLDEBUG'
} || 0;
BEGIN {
$ERROR
= 0;
if
( $@ ) {
}
$NUMTESTS
= 7;
plan
tests
=>
$NUMTESTS
;
}
ok 1;
my
$input
= Bio::SeqIO->new(
-file
=> File::Spec->catfile(
qw(t data NM_002254.gb)
),
-format
=>
'Genbank'
);
my
$seq
=
$input
->next_seq;
ok
my
$sirna
= Bio::Tools::SiRNA->new(
-target
=>
$seq
,
);
my
@pairs
=
$sirna
->design;
ok
scalar
(
@pairs
), 65,
"CDS only: got "
.
scalar
(
@pairs
) ;
my
@feats
=
$seq
->remove_SeqFeatures;
foreach
my
$feat
(
@feats
) {
$seq
->add_SeqFeature(
$feat
)
unless
(
$feat
->primary_tag eq
'Target'
or
$feat
->isa(
'Bio::SeqFeature::SiRNA::Pair'
));
}
ok
$sirna
->include_3pr(1);
@pairs
=
$sirna
->design;
print
"With 3p UTR: got "
,
scalar
(
@pairs
),
"\n"
if
$DEBUG
;
ok
scalar
(
@pairs
), 140;
my
$newseq
= Bio::Seq->new(
-seq
=>
$seq
->seq);
ok
$sirna
->target(
$newseq
);
@pairs
=
$sirna
->design;
print
"Bare sequence: got "
,
scalar
(
@pairs
),
"\n"
if
$DEBUG
;
ok
scalar
(
@pairs
), 142;