Commit 2321b0a1 authored by Marek Szuba's avatar Marek Szuba
Browse files

Change the RNAProduct stable-ID prefix from ENSM to ENSS

See ENSCORESW-3054. Only really affects the test suite at this point,
in the code proper the prefix only appears in docstrings.
parent def3181b
......@@ -217,7 +217,7 @@ sub fetch_by_dbID {
Arg [1] : string $stable_id
The stable identifier of the RNAProduct to obtain
Example : $rnaproduct = $rnaproduct_adaptor->fetch_by_stable_id("ENSM00001");
Example : $rnaproduct = $rnaproduct_adaptor->fetch_by_stable_id("ENSS00001");
Description: This fetches a RNAProduct object via its stable id.
Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
found.
......
......@@ -48,7 +48,7 @@ members.
);
# Stable-ID setter
$miR->stable_id('ENSM00090210');
$miR->stable_id('ENSS00090210');
# Get start and end position in the precursor transcript
my $start = $miR->start();
......
......@@ -48,7 +48,7 @@ commonly play a role in gene expression.
);
# Stable-ID setter
$rnaproduct->stable_id('ENSM00090210');
$rnaproduct->stable_id('ENSS00090210');
# Get start and end position in the precursor transcript
my $start = $rnaproduct->start();
......@@ -708,7 +708,7 @@ sub seq {
=head2 stable_id
Arg [1] : (optional) string $stable_id - stable ID to set
Example : $rnaproduct->stable_id('ENSM00090210');
Example : $rnaproduct->stable_id('ENSS00090210');
Description: Getter/setter for attribute stable_id.
Unlike stable_id_version(), setting a new stable ID does NOT
reset the version number.
......@@ -731,7 +731,7 @@ sub stable_id {
=head2 stable_id_version
Arg [1] : (optional) String - the stable ID with version to set
Example : $rnaproduct->stable_id("ENSM0059890.3");
Example : $rnaproduct->stable_id("ENSS0059890.3");
Description: Getter/setter for stable id with version for this RNAProduct.
If the input string omits the version part, the version gets reset
to undef; use stable_id() if you want to avoid this.
......
......@@ -103,7 +103,7 @@ ok($rp, 'RNAProduct constructor works without arguments');
end => 456,
start_exon => $exon1,
end_exon => $exon2,
stable_id => 'ENSM00012345',
stable_id => 'ENSS00012345',
version => 1337,
dbID => 314,
seq => 'ACGTACGT',
......@@ -283,7 +283,7 @@ $rp = $rp_a->fetch_by_dbID(1);
ok($rp, 'Can fetch RNAProduct by dbID');
$rp = undef;
$rp = $rp_a->fetch_by_stable_id('ENSM00000000001');
$rp = $rp_a->fetch_by_stable_id('ENSS00000000001');
ok($rp, 'Can fetch RNAProduct by stable ID');
isa_ok($rp, 'Bio::EnsEMBL::MicroRNA', 'miRNA object from database');
......@@ -312,7 +312,7 @@ subtest 'Exon links' => sub {
is($rp->start_Exon()->stable_id(), 'ENSE00000111112', 'Start exon has expected stable ID');
is($rp->end_Exon()->stable_id() , 'ENSE00000111112', 'End exon has expected stable ID');
my $rp_no_exons = $rp_a->fetch_by_stable_id('ENSM00000000002');
my $rp_no_exons = $rp_a->fetch_by_stable_id('ENSS00000000002');
is($rp_no_exons->start_Exon(), undef, 'Can correctly handle RNAProduct with no start exon');
is($rp_no_exons->end_Exon() , undef, 'Can correctly handle RNAProduct with no end exon');
};
......@@ -433,7 +433,7 @@ subtest 'Write operations' => sub {
my %insert_args = (
start => 6,
end => 27,
stable_id => 'ENSM00000000099',
stable_id => 'ENSS00000000099',
version => 1,
created_date => time(),
modified_date => time(),
......
1 2 21717 46 162035 67 162035 ENSM00000000001 1 2018-05-14 12:00:00 2018-05-14 12:00:00
2 2 21717 7 \N 28 \N ENSM00000000002 1 2018-05-21 17:00:00 2018-05-21 17:00:00
1 2 21717 46 162035 67 162035 ENSS00000000001 1 2018-05-14 12:00:00 2018-05-14 12:00:00
2 2 21717 7 \N 28 \N ENSS00000000002 1 2018-05-21 17:00:00 2018-05-21 17:00:00
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