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"""This contains all the necessary functions that are required to add traits
to the published database"""
from dataclasses import dataclass
from typing import Any, Dict, Optional
@dataclass(frozen=True)
class Riset:
"""Class for keeping track of riset. A riset is a group e.g. rat HSNIH-Palmer,
BXD
"""
name: Optional[str]
r_id: Optional[int]
@dataclass(frozen=True)
class WebqtlCaseData:
"""Class for keeping track of one case data in one trait"""
value: Optional[float] = None
variance: Optional[float] = None
count: Optional[int] = None # Number of Individuals
def __str__(self):
_str = ""
if self.value:
_str += f"value={self.value:.3f}"
if self.variance:
_str += f" variance={self.variance:.3f}"
if self.count:
_str += " n_data={self.count}"
return _str
def lookup_webqtldataset_name(riset_name: str, conn: Any):
"""Given a group name(riset), return it's name e.g. BXDPublish,
HLCPublish."""
with conn.cursor() as cursor:
cursor.execute(
"SELECT PublishFreeze.Name FROM "
"PublishFreeze, InbredSet WHERE "
"PublishFreeze.InbredSetId = InbredSet.Id "
"AND InbredSet.Name = '%s'" % riset_name)
_result, *_ = cursor.fetchone()
return _result
def get_riset(data_type: str, name: str, conn: Any):
"""Get the groups given the data type and it's PublishFreeze or GenoFreeze
name
"""
query, _name, _id = None, None, None
if data_type == "Publish":
query = ("SELECT InbredSet.Name, InbredSet.Id FROM InbredSet, "
"PublishFreeze WHERE PublishFreeze.InbredSetId = "
"InbredSet.Id AND PublishFreeze.Name = '%s'" % name)
elif data_type == "Geno":
query = ("SELECT InbredSet.Name, InbredSet.Id FROM InbredSet, "
"GenoFreeze WHERE GenoFreeze.InbredSetId = "
"InbredSet.Id AND GenoFreeze.Name = '%s'" % name)
elif data_type == "ProbeSet":
query = ("SELECT InbredSet.Name, InbredSet.Id FROM "
"InbredSet, ProbeSetFreeze, ProbeFreeze WHERE "
"ProbeFreeze.InbredSetId = InbredSet.Id AND "
"ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND "
"ProbeSetFreeze.Name = '%s'" % name)
if query:
with conn.cursor() as cursor:
_name, _id = cursor.fetchone()
if _name == "BXD300":
_name = "BXD"
return Riset(_name, _id)
def insert_publication(pubmed_id: int, publication: Optional[Dict],
conn: Any):
"""Creates a new publication record if it's not available"""
sql = ("SELECT Id FROM Publication where "
"PubMed_ID = %d" % pubmed_id)
_id = None
with conn.cursor() as cursor:
cursor.execute(sql)
_id = cursor.fetchone()
if not _id and publication:
# The Publication contains the fields: 'authors', 'title', 'abstract',
# 'journal','volume','pages','month','year'
insert_query = ("INSERT into Publication (%s) Values (%s)" %
(", ".join(publication.keys()),
", ".join(['%s'] * len(publication))))
with conn.cursor() as cursor:
cursor.execute(insert_query, tuple(publication.values()))
def retrieve_trait_dataset_name(trait_type, threshold, name, connection):
"""
Retrieve the name of a trait given the trait's name
This is extracted from the `webqtlDataset.retrieveName` function as is
implemented at
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169
"""
columns = "Id, Name, FullName, ShortName{}".format(
", DataScale" if trait_type == "ProbeSet" else "")
query = (
"SELECT {columns} "
"FROM {trait_type}Freeze "
"WHERE "
"public > %(threshold)s "
"AND "
"(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format(
columns=columns, trait_type=trait_type)
with connection.cursor() as cursor:
cursor.execute(query, {"threshold": threshold, "name": name})
return cursor.fetchone()
PUBLISH_TRAIT_INFO_QUERY = (
"SELECT "
"PublishXRef.Id, Publication.PubMed_ID, "
"Phenotype.Pre_publication_description, "
"Phenotype.Post_publication_description, "
"Phenotype.Original_description, "
"Phenotype.Pre_publication_abbreviation, "
"Phenotype.Post_publication_abbreviation, "
"Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, "
"Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), "
"Publication.Title, Publication.Abstract, Publication.Journal, "
"Publication.Volume, Publication.Pages, Publication.Month, "
"Publication.Year, PublishXRef.Sequence, Phenotype.Units, "
"PublishXRef.comments "
"FROM "
"PublishXRef, Publication, Phenotype, PublishFreeze "
"WHERE "
"PublishXRef.Id = %(trait_name)s AND "
"Phenotype.Id = PublishXRef.PhenotypeId AND "
"Publication.Id = PublishXRef.PublicationId AND "
"PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
"PublishFreeze.Id =%(trait_dataset_id)s")
def retrieve_publish_trait_info(trait_data_source, conn):
"""Retrieve trait information for type `Publish` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
with conn.cursor() as cursor:
cursor.execute(
PUBLISH_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_id"]
})
return cursor.fetchone()
PROBESET_TRAIT_INFO_QUERY = (
"SELECT "
"ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
"ProbeSet.probe_target_description, ProbeSet.chr, ProbeSet.mb, "
"ProbeSet.alias, ProbeSet.geneid, ProbeSet.genbankid, ProbeSet.unigeneid, "
"ProbeSet.omim, ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
"ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
"ProbeSet.strand_probe, ProbeSet.strand_gene, "
"ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
"ProbeSet.probe_set_specificity, ProbeSet.probe_set_blat_score, "
"ProbeSet.probe_set_blat_mb_start, ProbeSet.probe_set_blat_mb_end, "
"ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
"ProbeSet.flag "
"FROM "
"ProbeSet, ProbeSetFreeze, ProbeSetXRef "
"WHERE "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND "
"ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
"ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
"ProbeSet.Name = %(trait_name)s")
def retrieve_probeset_trait_info(trait_data_source, conn):
"""Retrieve trait information for type `ProbeSet` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
with conn.cursor() as cursor:
cursor.execute(
PROBESET_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_name"]
})
return cursor.fetchone()
GENO_TRAIT_INFO_QUERY = (
"SELECT "
"Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
"FROM "
"Geno, GenoFreeze, GenoXRef "
"WHERE "
"GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND "
"GenoFreeze.Name = %(trait_dataset_name)s AND Geno.Name = %(trait_name)s")
def retrieve_geno_trait_info(trait_data_source, conn):
"""Retrieve trait information for type `Geno` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
with conn.cursor() as cursor:
cursor.execute(
GENO_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_name"]
})
return cursor.fetchone()
TEMP_TRAIT_INFO_QUERY = (
"SELECT name, description FROM Temp "
"WHERE Name = %(trait_name)s")
def retrieve_temp_trait_info(trait_data_source, conn):
"""Retrieve trait information for type `Temp` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
with conn.cursor() as cursor:
cursor.execute(
TEMP_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name"]
})
return cursor.fetchone()
def retrieve_trait_info(
trait_type, trait_name, trait_dataset_id, trait_dataset_name, conn):
"""Retrieves the trait information.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
This function, or the dependent functions, might be incomplete as they are
currently."""
trait_info_function_table = {
"Publish": retrieve_publish_trait_info,
"ProbeSet": retrieve_probeset_trait_info,
"Geno": retrieve_geno_trait_info,
"Temp": retrieve_temp_trait_info
}
return trait_info_function_table[trait_type](
{
"trait_name": trait_name,
"trait_dataset_id": trait_dataset_id,
"trait_dataset_name":trait_dataset_name
},
conn)
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