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ensembl-gh-mirror
ensembl
Commits
2223def0
Commit
2223def0
authored
12 years ago
by
Andy Yates
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switching from ok to is & Test::More
parent
fb266ae2
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1 changed file
modules/t/operon_transcript.t
+42
-39
42 additions, 39 deletions
modules/t/operon_transcript.t
with
42 additions
and
39 deletions
modules/t/operon_transcript.t
+
42
−
39
View file @
2223def0
use
strict
;
use
warnings
;
BEGIN
{
$|
=
1
;
use
Test
;
plan
tests
=>
50
;
}
use
Test::
More
;
use
Bio::EnsEMBL::Test::
MultiTestDB
;
use
Bio::EnsEMBL::Test::
TestUtils
;
use
Bio::EnsEMBL::
Operon
;
...
...
@@ -21,6 +17,8 @@ ok(1);
my
$multi
=
Bio::EnsEMBL::Test::
MultiTestDB
->
new
();
$multi
->
save
('
core
',
'
operon
',
'
operon_transcript
',
'
gene
',
'
transcript
');
my
$dba
=
$multi
->
get_DBAdaptor
("
core
");
debug
("
Test database instatiated
");
...
...
@@ -40,7 +38,7 @@ my $operon = Bio::EnsEMBL::Operon->new( -START => $start,
-
STRAND
=>
$strand
,
-
SLICE
=>
$slice
,
-
DISPLAY_LABEL
=>
$display_label
,
-
STABLE_ID
=>
"
op1
",
-
ANALYSIS
=>
$analysis
);
ok
(
$analysis
,
$operon
->
analysis
()
,
"
Analysis
"
);
is
(
$analysis
,
$operon
->
analysis
());
my
$gene_name
=
"
accB
";
my
$gene_start
=
31225346
;
...
...
@@ -91,6 +89,7 @@ for my $feature ( $gene2, $transcript2, $exon2 ) {
$feature
->
slice
(
$slice
);
$feature
->
strand
(
$gene_strand
);
}
$gene2
->
analysis
(
$analysis
);
$transcript2
->
analysis
(
$analysis
);
$exon2
->
phase
(
0
);
...
...
@@ -122,7 +121,7 @@ my $operon_transcript =
$operon_transcript
->
add_gene
(
$gene
);
$operon_transcript
->
add_gene
(
$gene2
);
$operon
->
add_OperonTranscript
(
$operon_transcript
);
ok
(
$analysis
,
$operon_transcript
->
analysis
(),
"
Analysis
"
);
is
(
$analysis
,
$operon_transcript
->
analysis
(),
"
Analysis
"
);
my
$operon_transcript2
=
Bio::EnsEMBL::
OperonTranscript
->
new
(
-
START
=>
$start
,
...
...
@@ -131,7 +130,7 @@ my $operon_transcript2 =
-
SLICE
=>
$slice
,
-
STABLE_ID
=>
"
opt2
",
-
ANALYSIS
=>
$analysis
);
$operon_transcript2
->
add_gene
(
$gene
);
$operon
->
add_OperonTranscript
(
$operon_transcript2
);
ok
(
$analysis
,
$operon_transcript
->
analysis
(),
"
Analysis
"
);
is
(
$analysis
,
$operon_transcript
->
analysis
(),
"
Analysis
"
);
# store the lot
# store operon
...
...
@@ -140,69 +139,69 @@ ok( defined $operon->dbID() );
# retrieve operon
my
$operon2
=
$operon_adaptor
->
fetch_by_dbID
(
$operon
->
dbID
()
);
ok
(
$operon2
->
dbID
(),
$operon
->
dbID
(),
"
Operon ID
"
);
ok
(
$operon2
->
display_label
(),
$operon
->
display_label
(),
"
Operon name
"
);
ok
(
$operon2
->
seq_region_start
(),
$operon
->
seq_region_start
(),
"
Operon start
"
);
ok
(
$operon2
->
seq_region_end
(),
$operon
->
seq_region_end
(),
"
Operon end
"
);
ok
(
$operon2
->
seq_region_strand
(),
is
(
$operon2
->
dbID
(),
$operon
->
dbID
(),
"
Operon ID
"
);
is
(
$operon2
->
display_label
(),
$operon
->
display_label
(),
"
Operon name
"
);
is
(
$operon2
->
seq_region_start
(),
$operon
->
seq_region_start
(),
"
Operon start
"
);
is
(
$operon2
->
seq_region_end
(),
$operon
->
seq_region_end
(),
"
Operon end
"
);
is
(
$operon2
->
seq_region_strand
(),
$operon
->
seq_region_strand
(),
"
Operon strand
"
);
ok
(
$operon2
->
analysis
(),
$operon
->
analysis
(),
"
Analysis
"
);
is
(
$operon2
->
analysis
(),
$operon
->
analysis
(),
"
Analysis
"
);
my
@operon_transcripts
=
@
{
$operon2
->
get_all_OperonTranscripts
()
};
# check operon transcript
ok
(
scalar
@operon_transcripts
,
2
,
"
Expected number of transcripts
"
);
is
(
scalar
@operon_transcripts
,
2
,
"
Expected number of transcripts
"
);
my
$operon_transcript_r
=
$operon_transcripts
[
0
];
ok
(
$operon_transcript_r
->
dbID
(),
$operon_transcript
->
dbID
(),
is
(
$operon_transcript_r
->
dbID
(),
$operon_transcript
->
dbID
(),
"
Operon transcript ID
"
);
ok
(
$operon_transcript_r
->
seq_region_start
(),
is
(
$operon_transcript_r
->
seq_region_start
(),
$operon_transcript
->
seq_region_start
(),
"
Operon transcript start
"
);
ok
(
$operon_transcript_r
->
seq_region_end
(),
is
(
$operon_transcript_r
->
seq_region_end
(),
$operon_transcript
->
seq_region_end
(),
"
Operon transcript end
"
);
ok
(
$operon_transcript_r
->
seq_region_strand
(),
is
(
$operon_transcript_r
->
seq_region_strand
(),
$operon_transcript
->
seq_region_strand
(),
"
Operon transcript strand
"
);
ok
(
$operon_transcript
->
analysis
(),
$operon_transcript_r
->
analysis
(),
"
Analysis
"
);
is
(
$operon_transcript
->
analysis
(),
$operon_transcript_r
->
analysis
(),
"
Analysis
"
);
# check genes
my
@ogenes
=
@
{
$operon_transcript_r
->
get_all_Genes
()
};
ok
(
scalar
@ogenes
,
2
,
"
Expected number of genes
"
);
is
(
scalar
@ogenes
,
2
,
"
Expected number of genes
"
);
my
$gene_r
=
$ogenes
[
0
];
ok
(
$gene_r
->
dbID
(),
$gene
->
dbID
(),
"
Gene ID
"
);
ok
(
$gene_r
->
seq_region_start
(),
$gene
->
seq_region_start
(),
"
Gene start
"
);
ok
(
$gene_r
->
seq_region_end
(),
$gene
->
seq_region_end
(),
"
Gene end
"
);
ok
(
$gene_r
->
seq_region_strand
(),
$gene
->
seq_region_strand
(),
"
Gene strand
"
);
is
(
$gene_r
->
dbID
(),
$gene
->
dbID
(),
"
Gene ID
"
);
is
(
$gene_r
->
seq_region_start
(),
$gene
->
seq_region_start
(),
"
Gene start
"
);
is
(
$gene_r
->
seq_region_end
(),
$gene
->
seq_region_end
(),
"
Gene end
"
);
is
(
$gene_r
->
seq_region_strand
(),
$gene
->
seq_region_strand
(),
"
Gene strand
"
);
$gene_r
=
$ogenes
[
1
];
ok
(
$gene_r
->
dbID
(),
$gene2
->
dbID
(),
"
Gene ID
"
);
ok
(
$gene_r
->
seq_region_start
(),
$gene2
->
seq_region_start
(),
"
Gene start
"
);
ok
(
$gene_r
->
seq_region_end
(),
$gene2
->
seq_region_end
(),
"
Gene end
"
);
ok
(
$gene_r
->
seq_region_strand
(),
$gene2
->
seq_region_strand
(),
"
Gene strand
"
);
is
(
$gene_r
->
dbID
(),
$gene2
->
dbID
(),
"
Gene ID
"
);
is
(
$gene_r
->
seq_region_start
(),
$gene2
->
seq_region_start
(),
"
Gene start
"
);
is
(
$gene_r
->
seq_region_end
(),
$gene2
->
seq_region_end
(),
"
Gene end
"
);
is
(
$gene_r
->
seq_region_strand
(),
$gene2
->
seq_region_strand
(),
"
Gene strand
"
);
my
$operon_transcript_r2
=
$operon_transcripts
[
1
];
ok
(
$operon_transcript_r2
->
dbID
(),
is
(
$operon_transcript_r2
->
dbID
(),
$operon_transcript2
->
dbID
(),
"
Operon transcript ID
"
);
ok
(
$operon_transcript_r2
->
seq_region_start
(),
is
(
$operon_transcript_r2
->
seq_region_start
(),
$operon_transcript2
->
seq_region_start
(),
"
Operon transcript start
"
);
ok
(
$operon_transcript_r2
->
seq_region_end
(),
is
(
$operon_transcript_r2
->
seq_region_end
(),
$operon_transcript2
->
seq_region_end
(),
"
Operon transcript end
"
);
ok
(
$operon_transcript_r2
->
seq_region_strand
(),
is
(
$operon_transcript_r2
->
seq_region_strand
(),
$operon_transcript2
->
seq_region_strand
(),
"
Operon transcript strand
"
);
ok
(
$operon_transcript2
->
analysis
(),
$operon_transcript_r2
->
analysis
(),
"
Analysis
"
);
is
(
$operon_transcript2
->
analysis
(),
$operon_transcript_r2
->
analysis
(),
"
Analysis
"
);
# check genes
@ogenes
=
@
{
$operon_transcript_r2
->
get_all_Genes
()
};
ok
(
scalar
@ogenes
,
1
,
"
Expected number of genes
"
);
is
(
scalar
@ogenes
,
1
,
"
Expected number of genes
"
);
$gene_r
=
$ogenes
[
0
];
ok
(
$gene_r
->
dbID
(),
$gene
->
dbID
(),
"
Gene ID
"
);
ok
(
$gene_r
->
seq_region_start
(),
$gene
->
seq_region_start
(),
"
Gene start
"
);
ok
(
$gene_r
->
seq_region_end
(),
$gene
->
seq_region_end
(),
"
Gene end
"
);
ok
(
$gene_r
->
seq_region_strand
(),
$gene
->
seq_region_strand
(),
"
Gene strand
"
);
is
(
$gene_r
->
dbID
(),
$gene
->
dbID
(),
"
Gene ID
"
);
is
(
$gene_r
->
seq_region_start
(),
$gene
->
seq_region_start
(),
"
Gene start
"
);
is
(
$gene_r
->
seq_region_end
(),
$gene
->
seq_region_end
(),
"
Gene end
"
);
is
(
$gene_r
->
seq_region_strand
(),
$gene
->
seq_region_strand
(),
"
Gene strand
"
);
$dba
->
get_OperonAdaptor
()
->
remove
(
$operon
);
$dba
->
get_GeneAdaptor
()
->
remove
(
$gene
);
...
...
@@ -228,3 +227,7 @@ ok( scalar(@operon_transcripts) == 1 );
debug
("
OperonTranscript->list_stable_ids
");
my
$stable_ids
=
$ota
->
list_stable_ids
();
ok
(
@
{
$stable_ids
});
$multi
->
restore
('
core
');
done_testing
();
\ No newline at end of file
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