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"Dataset Group class ..."
import os
import json
from base import webqtlConfig
from .markers import Markers, HumanMarkers
from utility import webqtlUtil
from utility import gen_geno_ob
from db import webqtlDatabaseFunction
from maintenance import get_group_samplelists
from wqflask.database import database_connection
from utility.tools import (
locate,
USE_REDIS,
flat_files,
get_setting,
flat_file_exists,
locate_ignore_error)
class DatasetGroup:
"""
Each group has multiple datasets; each species has multiple groups.
For example, Mouse has multiple groups (BXD, BXA, etc), and each group
has multiple datasets associated with it.
"""
def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
if not name:
cursor.execute(dataset.query_for_group,
(dataset.name,))
else:
cursor.execute(
"SELECT InbredSet.Name, "
"InbredSet.Id, "
"InbredSet.GeneticType, "
"InbredSet.InbredSetCode "
"FROM InbredSet WHERE Name = %s",
(name,))
results = cursor.fetchone()
if results:
(self.name, self.id, self.genetic_type, self.code) = results
else:
self.name = name or dataset.name
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
self._datasets = None
self.genofile = None
def get_mapping_methods(self):
mapping_id = ()
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT MappingMethodId FROM "
"InbredSet WHERE Name= %s",
(self.name,))
results = cursor.fetchone()
if results and results[0]:
mapping_id = results[0]
if mapping_id == "1":
mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
elif mapping_id == "2":
mapping_names = ["GEMMA"]
elif mapping_id == "3":
mapping_names = ["R/qtl"]
elif mapping_id == "4":
mapping_names = ["GEMMA", "PLINK"]
else:
mapping_names = []
return mapping_id, mapping_names
def get_markers(self):
def check_plink_gemma():
if flat_file_exists("mapping"):
MAPPING_PATH = flat_files("mapping") + "/"
if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
return True
return False
if check_plink_gemma():
marker_class = HumanMarkers
else:
marker_class = Markers
if self.genofile:
self.markers = marker_class(self.genofile[:-5])
else:
self.markers = marker_class(self.name)
def get_f1_parent_strains(self):
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
except KeyError:
f1 = f12 = maternal = paternal = None
if f1 and f12:
self.f1list = [f1, f12]
if maternal and paternal:
self.parlist = [maternal, paternal]
def get_study_samplelists(self):
study_sample_file = locate_ignore_error(
self.name + ".json", 'study_sample_lists')
try:
f = open(study_sample_file)
except:
return []
study_samples = json.load(f)
return study_samples
def get_genofiles(self):
jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
try:
f = open(jsonfile)
except:
return None
jsondata = json.load(f)
return jsondata['genofile']
def get_samplelist(self, redis_conn):
result = None
key = "samplelist:v3:" + self.name
if USE_REDIS:
result = redis_conn.get(key)
if result is not None:
self.samplelist = json.loads(result)
else:
genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
if genotype_fn:
self.samplelist = get_group_samplelists.get_samplelist(
"geno", genotype_fn)
else:
self.samplelist = None
if USE_REDIS:
redis_conn.set(key, json.dumps(self.samplelist))
redis_conn.expire(key, 60 * 5)
def all_samples_ordered(self):
result = []
lists = (self.parlist, self.f1list, self.samplelist)
[result.extend(l) for l in lists if l]
return result
def read_genotype_file(self, use_reaper=False):
'''Read genotype from .geno file instead of database'''
# genotype_1 is Dataset Object without parents and f1
# genotype_2 is Dataset Object with parents and f1 (not for intercross)
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
full_filename = str(
locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
else:
full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(
Mat=self.parlist[0], Pat=self.parlist[1]) # , F1=_f1)
else:
genotype_2 = genotype_1
# determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
genotype = genotype_2
else:
self.incparentsf1 = 0
genotype = genotype_1
self.samplelist = list(genotype.prgy)
return genotype
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