BEGIN
{
if
($@)
{
}
$NTESTS
= 26;
plan
tests
=>
$NTESTS
;
}
ok(1);
my
$inputfilename
= Bio::Root::IO->catfile(
"t"
,
"data"
,
"geneid_1.0.out"
);
my
$parser
= Bio::Tools::Geneid->new(
-file
=>
$inputfilename
);
my
@genes
;
while
(
my
$gene
=
$parser
->next_prediction)
{
push
(
@genes
,
$gene
);
}
my
@transcripts
=
$genes
[0]->transcripts;
my
@exons
=
$transcripts
[0]->exons;
ok(
$transcripts
[0]->seq_id,
'10'
);
ok(
$exons
[0]->seq_id,
'10'
);
ok(
$transcripts
[0]->source_tag,
'geneid'
);
ok(
$exons
[0]->source_tag,
'geneid'
);
ok(
$transcripts
[0]->primary_tag,
'transcript'
);
ok(
$exons
[0]->primary_tag,
'Initial'
);
ok(
scalar
(
$transcripts
[0]->exons), 2);
ok(
$transcripts
[0]->start, 6090);
ok(
$transcripts
[0]->end, 7276);
ok(
$transcripts
[0]->score, 36.87);
ok(
$transcripts
[0]->strand, 1);
ok(
$exons
[0]->start, 6090);
ok(
$exons
[0]->end, 6155);
ok(
$exons
[0]->score,
'1.40'
);
ok(
$exons
[0]->strand, 1);
my
(
$type
) =
$exons
[0]->get_tag_values(
'Type'
);
ok(
$type
,
'Initial'
);
my
(
$phase
) =
$exons
[0]->get_tag_values(
'phase'
);
ok(
$phase
, 0);
my
(
$end_phase
) =
$exons
[0]->get_tag_values(
'end_phase'
);
ok(
$end_phase
, 0);
my
(
$start_signal_score
) =
$exons
[0]->get_tag_values(
'start_signal_score'
);
ok(
$start_signal_score
, 2.15);
my
(
$end_signal_score
) =
$exons
[0]->get_tag_values(
'end_signal_score'
);
ok(
$end_signal_score
, 3.63);
my
(
$coding_potential_score
) =
$exons
[0]->get_tag_values(
'coding_potential_score'
);
ok(
$coding_potential_score
, 12.34);
my
(
$homology_score
) =
$exons
[0]->get_tag_values(
'homology_score'
);
ok(
$homology_score
,
'0.00'
);
ok(
scalar
(
@genes
), 3);
@transcripts
=
$genes
[1]->transcripts;
ok(
scalar
(
$transcripts
[0]->exons), 5);
@transcripts
=
$genes
[2]->transcripts;
ok(
scalar
(
$transcripts
[0]->exons), 1);