diff options
Diffstat (limited to 'wqflask/base/data_set/datasetgroup.py')
| -rw-r--r-- | wqflask/base/data_set/datasetgroup.py | 193 |
1 files changed, 193 insertions, 0 deletions
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py new file mode 100644 index 00000000..a13d2f93 --- /dev/null +++ b/wqflask/base/data_set/datasetgroup.py @@ -0,0 +1,193 @@ +"Dataset Group class ..." + +import os +import json + + +from base import webqtlConfig +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, + 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() 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", + (dataset.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() 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 |