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"GenotypeDataSet class ..."
from .dataset import DataSet
from gn2.utility import webqtlUtil
from gn2.utility.tools import get_setting
from gn2.db import webqtlDatabaseFunction
from .utils import geno_mrna_confidentiality
from gn2.wqflask.database import database_connection
class GenotypeDataSet(DataSet):
def setup(self):
# Fields in the database table
self.search_fields = ['Name',
'Chr']
# Find out what display_fields is
self.display_fields = ['name',
'chr',
'mb',
'source2',
'sequence']
# Fields displayed in the search results table header
self.header_fields = ['Index',
'ID',
'Location']
# Todo: Obsolete or rename this field
self.type = 'Geno'
self.query_for_group = """
SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
FROM InbredSet, GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id AND
GenoFreeze.Name = %s"""
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
def get_trait_info(self, trait_list, species=None):
for this_trait in trait_list:
if not this_trait.haveinfo:
this_trait.retrieveInfo()
if this_trait.chr and this_trait.mb:
this_trait.location_repr = 'Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
def retrieve_sample_data(self, trait):
results = []
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT Strain.Name, GenoData.value, "
"GenoSE.error, NULL, Strain.Name2 "
"FROM (GenoData, GenoFreeze, Strain, Geno, "
"GenoXRef) LEFT JOIN GenoSE ON "
"(GenoSE.DataId = GenoData.Id AND "
"GenoSE.StrainId = GenoData.StrainId) "
"WHERE Geno.SpeciesId = %s AND "
"Geno.Name = %s AND GenoXRef.GenoId = Geno.Id "
"AND GenoXRef.GenoFreezeId = GenoFreeze.Id "
"AND GenoFreeze.Name = %s AND "
"GenoXRef.DataId = GenoData.Id "
"AND GenoData.StrainId = Strain.Id "
"ORDER BY Strain.Name",
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name,))
results = list(cursor.fetchall())
if self.group.name in webqtlUtil.ParInfo:
f1_1, f1_2, ref, nonref = webqtlUtil.ParInfo[self.group.name]
results.append([f1_1, 0, None, None, f1_1])
results.append([f1_2, 0, None, None, f1_2])
results.append([ref, -1, None, None, ref])
results.append([nonref, 1, None, None, nonref])
return results
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