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New column in results.nafeatureexpression #11

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merged 6 commits into from
Jan 6, 2025
Merged

New column in results.nafeatureexpression #11

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a373f92
Add column for raw counts to nafeatureexpression
kathryncrouch Dec 18, 2024
eee9a25
Add column for raw counts to nafeatureexpression
kathryncrouch Dec 18, 2024
625e9c8
Update column name
kathryncrouch Dec 18, 2024
5f77ef1
add isr and isrpm to intron junction table
jbrestel Dec 19, 2024
5aed09e
fix typo
mvnural Dec 20, 2024
fee8bde
fix formatting.
mvnural Dec 20, 2024
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1 change: 1 addition & 0 deletions Main/lib/sql/apidbschema/Oracle/createGusTuning.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -335,6 +335,7 @@ alter table results.GeneExpression add (percentile_channel2 FLOAT(126));
alter table results.NaFeatureExpression add (percentile_channel2 FLOAT(126));
alter table results.ReporterExpression add (percentile_channel2 FLOAT(126));
alter table results.RnaExpression add (percentile_channel2 FLOAT(126));
alter table results.NaFeatureExpression add (mean_raw_count FLOAT(126));

create index study.pan_info_ix
on study.ProtocolAppNode
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47 changes: 24 additions & 23 deletions Main/lib/sql/apidbschema/Oracle/createIntronJunction.sql
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Original file line number Diff line number Diff line change
@@ -1,27 +1,28 @@

CREATE TABLE apidb.IntronJunction (
intron_junction_id NUMBER(10),
protocol_app_node_id NUMBER(10) NOT NULL,
na_sequence_id NUMBER(10) NOT NULL,
segment_start NUMBER(10) NOT NULL,
segment_end NUMBER(10) NOT NULL,
is_reversed number(1),
unique_reads NUMBER(10),
nu_reads NUMBER(10),
MODIFICATION_DATE DATE,
USER_READ NUMBER(1),
USER_WRITE NUMBER(1),
GROUP_READ NUMBER(1),
GROUP_WRITE NUMBER(1),
OTHER_READ NUMBER(1),
OTHER_WRITE NUMBER(1),
ROW_USER_ID NUMBER(12),
ROW_GROUP_ID NUMBER(3),
ROW_PROJECT_ID NUMBER(4),
ROW_ALG_INVOCATION_ID NUMBER(12),
FOREIGN KEY (protocol_app_node_id) REFERENCES Study.ProtocolAppNode,
FOREIGN KEY (na_sequence_id) REFERENCES DoTS.NASequenceImp (NA_SEQUENCE_ID),
PRIMARY KEY (intron_junction_id)
intron_junction_id NUMBER(10),
protocol_app_node_id NUMBER(10) NOT NULL,
na_sequence_id NUMBER(10) NOT NULL,
segment_start NUMBER(10) NOT NULL,
segment_end NUMBER(10) NOT NULL,
is_reversed NUMBER(1),
unique_reads NUMBER(10),
nu_reads NUMBER(10),
isr NUMBER(10),
isrpm NUMBER(10),
MODIFICATION_DATE DATE,
USER_READ NUMBER(1),
USER_WRITE NUMBER(1),
GROUP_READ NUMBER(1),
GROUP_WRITE NUMBER(1),
OTHER_READ NUMBER(1),
OTHER_WRITE NUMBER(1),
ROW_USER_ID NUMBER(12),
ROW_GROUP_ID NUMBER(3),
ROW_PROJECT_ID NUMBER(4),
ROW_ALG_INVOCATION_ID NUMBER(12),
FOREIGN KEY (protocol_app_node_id) REFERENCES Study.ProtocolAppNode,
FOREIGN KEY (na_sequence_id) REFERENCES DoTS.NASequenceImp(NA_SEQUENCE_ID),
PRIMARY KEY (intron_junction_id)
);

CREATE SEQUENCE apidb.IntronJunction_sq;
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1 change: 1 addition & 0 deletions Main/lib/sql/apidbschema/Postgres/createGusTuning.sql
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Expand Up @@ -182,6 +182,7 @@ ALTER TABLE results.geneexpression ADD percentile_channel2 float8;
ALTER TABLE results.nafeatureexpression ADD percentile_channel2 float8;
ALTER TABLE results.reporterexpression ADD percentile_channel2 float8;
ALTER TABLE results.rnaexpression ADD percentile_channel2 float8;
ALTER TABLE results.nafeatureexpression ADD mean_raw_count float8;

CREATE INDEX pan_info_ix ON study.protocolappnode (protocol_app_node_id, isa_type, type_id, name, external_database_release_id, source_id, subtype_id, node_order_num);

Expand Down
49 changes: 25 additions & 24 deletions Main/lib/sql/apidbschema/Postgres/createIntronJunction.sql
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Original file line number Diff line number Diff line change
@@ -1,27 +1,28 @@

CREATE TABLE apidb.IntronJunction (
intron_junction_id NUMERIC(10),
protocol_app_node_id NUMERIC(10) NOT NULL,
na_sequence_id NUMERIC(10) NOT NULL,
segment_start NUMERIC(10) NOT NULL,
segment_end NUMERIC(10) NOT NULL,
is_reversed NUMERIC(1),
unique_reads NUMERIC(10),
nu_reads NUMERIC(10),
MODIFICATION_DATE TIMESTAMP,
USER_READ NUMERIC(1),
USER_WRITE NUMERIC(1),
GROUP_READ NUMERIC(1),
GROUP_WRITE NUMERIC(1),
OTHER_READ NUMERIC(1),
OTHER_WRITE NUMERIC(1),
ROW_USER_ID NUMERIC(12),
ROW_GROUP_ID NUMERIC(3),
ROW_PROJECT_ID NUMERIC(4),
ROW_ALG_INVOCATION_ID NUMERIC(12),
FOREIGN KEY (protocol_app_node_id) REFERENCES Study.ProtocolAppNode,
FOREIGN KEY (na_sequence_id) REFERENCES DoTS.NASequenceImp (NA_SEQUENCE_ID),
PRIMARY KEY (intron_junction_id)
intron_junction_id NUMERIC(10),
protocol_app_node_id NUMERIC(10) NOT NULL,
na_sequence_id NUMERIC(10) NOT NULL,
segment_start NUMERIC(10) NOT NULL,
segment_end NUMERIC(10) NOT NULL,
is_reversed NUMERIC(1),
unique_reads NUMERIC(10),
nu_reads NUMERIC(10),
isr NUMERIC(10),
isrpm NUMERIC(10),
MODIFICATION_DATE TIMESTAMP,
USER_READ NUMERIC(1),
USER_WRITE NUMERIC(1),
GROUP_READ NUMERIC(1),
GROUP_WRITE NUMERIC(1),
OTHER_READ NUMERIC(1),
OTHER_WRITE NUMERIC(1),
ROW_USER_ID NUMERIC(12),
ROW_GROUP_ID NUMERIC(3),
ROW_PROJECT_ID NUMERIC(4),
ROW_ALG_INVOCATION_ID NUMERIC(12),
FOREIGN KEY (protocol_app_node_id) REFERENCES Study.ProtocolAppNode,
FOREIGN KEY (na_sequence_id) REFERENCES DoTS.NASequenceImp(NA_SEQUENCE_ID),
PRIMARY KEY (intron_junction_id)
);

CREATE SEQUENCE apidb.IntronJunction_sq;
Expand Down Expand Up @@ -53,4 +54,4 @@ FROM
WHERE 'intronjunction' NOT IN (SELECT lower(name) FROM core.TableInfo
WHERE database_id = d.database_id);

------------------------------------------------------------------------------
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