diff options
Diffstat (limited to 'gn3/db/correlations.py')
| -rw-r--r-- | gn3/db/correlations.py | 147 |
1 files changed, 147 insertions, 0 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index f327dc3..ff570b4 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -379,3 +379,150 @@ def check_symbol_for_tissue_correlation( return True return False + +def fetch_sample_ids( + conn: Any, sample_names: Tuple[str, ...], species_name: str) -> Tuple[ + int, ...]: + """ + Given a sequence of sample names, and a species name, return the sample ids + that correspond to both. + + This is a partial migration of the + `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in + GeneNetwork1. + """ + query = ( + "SELECT Strain.Id FROM Strain, Species " + "WHERE Strain.Name IN %(samples_names)s " + "AND Strain.SpeciesId=Species.Id " + "AND Species.name=%(species_name)s") + with conn.cursor() as cursor: + cursor.execute( + query, samples_names=tuple(samples), + species_name=species) + return cursor.fetchall() + +def fetch_all_database_data( + conn: Any, species: str, gene_id: int, gene_symbol: str, + samples: Tuple[str, ...], db_type: str, db_name: str, method: str, + returnNumber: int, tissueProbeSetFreezeId: int) -> Tuple[Any, Any]: + """ + This is a migration of the + `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in + GeneNetwork1. + """ + def __build_query_sgo_lit__(temp_table, sample_id_columns, joins): + return ( + (f"SELECT {db_type}.Name, {temp_table}.value " + + sample_id_columns + + f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " + + f"LEFT JOIN {temp_table} ON {temp_table}.GeneId2=ProbeSet.GeneId " + + " ".join(joins) + + f" WHERE ProbeSet.GeneId IS NOT NULL " + + f"AND {temp_table}.value IS NOT NULL " + + f"AND {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " + + f"AND {db_type}Freeze.Name = %(db_name)s " + + f"AND {db_type}.Id = {db_type}XRef.{db_type}Id " + + f"ORDER BY {db_type}.Id"), + 2) + + def __build_query_tissue_corr__(temp_table, sample_id_columns, joins): + return ( + (f"SELECT {db_type}.Name, {temp_table}.Correlation, " + + f"{temp_table}.PValue, " + + sample_id_columns + + f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " + + f"LEFT JOIN {temp_table} ON {temp_table}.Symbol=ProbeSet.Symbol " + + " ".join(joins) + + f" WHERE ProbeSet.Symbol IS NOT NULL " + + f"AND {temp_table}.Correlation IS NOT NULL " + + f"AND {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " + + f"AND {db_type}Freeze.Name = %(db_name)s " + + f"AND {db_type}.Id = {db_type}XRef.%sId " + f"ORDER BY {db_type}.Id"), + 3) + + def __build_query__(sample_ids, temp_table): + sample_id_columns = ", ".join(f"T{smpl}.value" for smpl in samples_ids) + if db_type == "Publish": + joins = tuple( + ("LEFT JOIN PublishData AS T{item} " + "ON T{item}.Id = PublishXRef.DataId " + "AND T{item}.StrainId = %(T{item}_sample_id)s") + for item in sample_ids) + return ( + ("SELECT PublishXRef.Id, " + + sample_id_columns + + "FROM (PublishXRef, PublishFreeze) " + + " ".join(joins) + + " WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId " + "AND PublishFreeze.Name = %(db_name)s"), + 1) + if temp_table is not None: + joins = tuple( + ("LEFT JOIN {db_type}Data AS T{item} " + "ON T{item}.Id = {db_type}XRef.DataId " + "AND T{item}.StrainId=%(T{item}_sample_id)s") + for item in sample_ids) + if method.lower() == "sgo literature correlation": + return __build_query_sgo_lit__( + sample_ids, temp_table, sample_id_columns) + if method.lower() in ( + "tissue correlation, pearson's r", + "tissue correlation, spearman's rho"): + return __build_query_tissue_corr__( + sample_ids, temp_table, sample_id_columns) + joins = tuple( + (f"LEFT JOIN {db_type}Data AS T{item} " + f"ON T{item}.Id = {db_type}XRef.DataId " + f"AND T{item}.StrainId = %(T{item}_sample_id)s") + for item in sample_ids) + return ( + ( + f"SELECT {db_type}.Name, " + + sample_id_columns + + f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " + + " ".join(joins) + + f" WHERE {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " + + f"AND {db_type}Freeze.Name = %(db_name)s " + + f"AND {db_type}.Id = {db_type}XRef.{db_type}Id " + + f"ORDER BY {db_type}.Id"), + 1) + + def __fetch_data__(sample_ids, temp_table): + query, data_start_pos = __build_query__(sample_ids, temp_table) + with conn.cursor() as cursor: + cursor.execute( + query, db_name=db_name, + **{f"T{item}_sample_id": item for item in sample_ids}) + return cursor.fetchall() + + sample_ids = tuple( + # look into graduating this to an argument and removing the `samples` + # and `species` argument: function currying and compositions might help + # with this + f"{sample_id}" for sample_id in + fetch_sample_ids(conn, samples, species)) + + temp_table = None + if gene_id and db_type == "probeset": + if method.lower() == "sgo literature correlation": + temp_table = build_temporary_literature_table( + conn, species, gene_id, return_number) + if method.lower() in ( + "tissue correlation, pearson's r", + "tissue correlation, spearman's rho"): + temp_table = build_temporary_tissue_correlations_table( + conn, trait_symbol, probeset_freeze_id, method, return_number) + + trait_database = tuple( + item for sublist in + (__fetch_data__(ssample_ids, temp_table) + for ssample_ids in partition_all(25, sample_ids)) + for item in sublist) + + if temp_table: + with conn.cursor() as cursor: + cursor.execute(f"DROP TEMPORARY TABLE {temp_table}") + + return trait_database, data_start_pos |