diff options
Diffstat (limited to 'wqflask/base/data_set/datasetgroup.py')
| -rw-r--r-- | wqflask/base/data_set/datasetgroup.py | 195 |
1 files changed, 0 insertions, 195 deletions
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py deleted file mode 100644 index 95dc976f..00000000 --- a/wqflask/base/data_set/datasetgroup.py +++ /dev/null @@ -1,195 +0,0 @@ -"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 |