diff options
| -rw-r--r-- | gn3/db/traits.py | 245 |
1 files changed, 244 insertions, 1 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index be46437..a740352 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,5 +1,5 @@ """This class contains functions relating to trait data manipulation""" -from typing import Any, Dict, Union +from typing import Any, Dict, Union, Sequence from gn3.function_helpers import compose from gn3.db.datasets import retrieve_trait_dataset @@ -408,3 +408,246 @@ def retrieve_trait_info( "riset": trait_dataset["riset"] } return trait_info + +def retrieve_temp_trait_data(trait_info: dict, conn: Any): + """ + Retrieve trait data for `Temp` traits. + """ + query = ( + "SELECT " + "Strain.Name, TempData.value, TempData.SE, TempData.NStrain, " + "TempData.Id " + "FROM TempData, Temp, Strain " + "WHERE TempData.StrainId = Strain.Id " + "AND TempData.Id = Temp.DataId " + "AND Temp.name = %(trait_name)s " + "ORDER BY Strain.Name") + with conn.cursor() as cursor: + cursor.execute( + query, + {"trait_name": trait_info["trait_name"]}) + return [dict(zip( + ["strain_name", "value", "se_error", "nstrain", "id"], row)) + for row in cursor.fetchall()] + return [] + +def retrieve_species_id(riset, conn: Any): + """ + Retrieve a species id given the RISet value + """ + with conn.cursor as cursor: + cursor.execute( + "SELECT SpeciesId from InbredSet WHERE Name = %(riset)s", + {"riset": riset}) + return cursor.fetchone()[0] + return None + +def retrieve_geno_trait_data(trait_info: Dict, conn: Any): + """ + Retrieve trait data for `Geno` traits. + """ + query = ( + "SELECT Strain.Name, GenoData.value, GenoSE.error, GenoData.Id " + "FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) " + "LEFT JOIN GenoSE ON " + "(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) " + "WHERE Geno.SpeciesId = %(species_id)s " + "AND Geno.Name = %(trait_name)s AND GenoXRef.GenoId = Geno.Id " + "AND GenoXRef.GenoFreezeId = GenoFreeze.Id " + "AND GenoFreeze.Name = %(dataset_name)s " + "AND GenoXRef.DataId = GenoData.Id " + "AND GenoData.StrainId = Strain.Id " + "ORDER BY Strain.Name") + with conn.cursor() as cursor: + cursor.execute( + query, + {"trait_name": trait_info["trait_name"], + "dataset_name": trait_info["db"]["dataset_name"], + "species_id": retrieve_species_id( + trait_info["db"]["riset"], conn)}) + return [dict(zip( + ["strain_name", "value", "se_error", "id"], row)) + for row in cursor.fetchall()] + return [] + +def retrieve_publish_trait_data(trait_info: Dict, conn: Any): + """ + Retrieve trait data for `Publish` traits. + """ + query = ( + "SELECT " + "Strain.Name, PublishData.value, PublishSE.error, NStrain.count, " + "PublishData.Id " + "FROM (PublishData, Strain, PublishXRef, PublishFreeze) " + "LEFT JOIN PublishSE ON " + "(PublishSE.DataId = PublishData.Id " + "AND PublishSE.StrainId = PublishData.StrainId) " + "LEFT JOIN NStrain ON " + "(NStrain.DataId = PublishData.Id " + "AND NStrain.StrainId = PublishData.StrainId) " + "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId " + "AND PublishData.Id = PublishXRef.DataId " + "AND PublishXRef.Id = %(trait_name)s " + "AND PublishFreeze.Id = %(dataset_id)s " + "AND PublishData.StrainId = Strain.Id " + "ORDER BY Strain.Name") + with conn.cursor() as cursor: + cursor.execute( + query, + {"trait_name": trait_info["trait_name"], + "dataset_id": trait_info["db"]["dataset_id"]}) + return [dict(zip( + ["strain_name", "value", "se_error", "nstrain", "id"], row)) + for row in cursor.fetchall()] + return [] + +def retrieve_cellid_trait_data(trait_info: Dict, conn: Any): + """ + Retrieve trait data for `Probe Data` types. + """ + query = ( + "SELECT " + "Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id " + "FROM (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain," + " Probe, ProbeSet) " + "LEFT JOIN ProbeSE ON " + "(ProbeSE.DataId = ProbeData.Id " + " AND ProbeSE.StrainId = ProbeData.StrainId) " + "WHERE Probe.Name = %(cellid)s " + "AND ProbeSet.Name = %(trait_name)s " + "AND Probe.ProbeSetId = ProbeSet.Id " + "AND ProbeXRef.ProbeId = Probe.Id " + "AND ProbeXRef.ProbeFreezeId = ProbeFreeze.Id " + "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " + "AND ProbeSetFreeze.Name = %(dataset_name)s " + "AND ProbeXRef.DataId = ProbeData.Id " + "AND ProbeData.StrainId = Strain.Id " + "ORDER BY Strain.Name") + with conn.cursor() as cursor: + cursor.execute( + query, + {"cellid": trait_info["cellid"], + "trait_name": trait_info["trait_name"], + "dataset_id": trait_info["db"]["dataset_id"]}) + return [dict(zip( + ["strain_name", "value", "se_error", "id"], row)) + for row in cursor.fetchall()] + return [] + +def retrieve_probeset_trait_data(trait_info: Dict, conn: Any): + """ + Retrieve trait data for `ProbeSet` traits. + """ + query = ( + "SELECT Strain.Name, ProbeSetData.value, ProbeSetSE.error, " + "ProbeSetData.Id " + "FROM (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) " + "LEFT JOIN ProbeSetSE ON " + "(ProbeSetSE.DataId = ProbeSetData.Id " + "AND ProbeSetSE.StrainId = ProbeSetData.StrainId) " + "WHERE ProbeSet.Name = %(trait_name)s " + "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id " + "AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " + "AND ProbeSetFreeze.Name = %(dataset_name)s " + "AND ProbeSetXRef.DataId = ProbeSetData.Id " + "AND ProbeSetData.StrainId = Strain.Id " + "ORDER BY Strain.Name") + + with conn.cursor() as cursor: + cursor.execute( + query, + {"trait_name": trait_info["trait_name"], + "dataset_name": trait_info["db"]["dataset_name"]}) + return [dict(zip( + ["strain_name", "value", "se_error", "id"], row)) + for row in cursor.fetchall()] + return [] + +def with_strainlist_data_setup(strainlist: Sequence[str]): + """ + Build function that computes the trait data from provided list of strains. + + PARAMETERS + strainlist: (list) + A list of strain names + + RETURNS: + Returns a function that given some data from the database, computes the + strain's value, variance and ndata values, only if the strain is present + in the provided `strainlist` variable. + """ + def setup_fn(tdata): + if tdata["strain_name"] in strainlist: + val = tdata["value"] + if val is not None: + return { + "strain_name": tdata["strain_name"], + "value": val, + "variance": tdata["se_error"], + "ndata": tdata.get("nstrain", None) + } + return None + return setup_fn + +def without_strainlist_data_setup(): + """ + Build function that computes the trait data. + + RETURNS: + Returns a function that given some data from the database, computes the + strain's value, variance and ndata values. + """ + def setup_fn(tdata): + val = tdata["value"] + if val is not None: + return { + "strain_name": tdata["strain_name"], + "value": val, + "variance": tdata["se_error"], + "ndata": tdata.get("nstrain", None) + } + return None + return setup_fn + +def retrieve_trait_data(trait: dict, conn: Any, strainlist: Sequence[str] = tuple()): + """ + Retrieve trait data + + DESCRIPTION + Retrieve trait data as is done in + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L258-L386 + """ + # I do not like this section, but it retains the flow in the old codebase + if trait["db"]["dataset_type"] == "Temp": + results = retrieve_temp_trait_data(trait, conn) + elif trait["db"]["dataset_type"] == "Publish": + results = retrieve_publish_trait_data(trait, conn) + elif trait["cellid"]: + results = retrieve_cellid_trait_data(trait, conn) + elif trait["db"]["dataset_type"] == "ProbeSet": + results = retrieve_probeset_trait_data(trait, conn) + else: + results = retrieve_geno_trait_data(trait, conn) + + if results: + # do something with mysqlid + mysqlid = results[0]["id"] + if strainlist: + data = [ + item for item in + map(with_strainlist_data_setup(strainlist), results) + if item is not None] + else: + data = [ + item for item in + map(without_strainlist_data_setup(), results) + if item is not None] + + return { + "mysqlid": mysqlid, + "data": dict(map( + lambda x: ( + x["strain_name"], + {k:v for k, v in x.items() if x != "strain_name"}), + data))} + return {} |