def buildFiles(self, weight_db_logic):
do_correlations = self.correlation_output is not None
if do_correlations:
if os.path.exists(self.correlation_output):
logging.info("%s already exists, delete it if you want it figured out again", self.correlation_output)
do_correlations = False
else:
correlation_dir = os.path.dirname(self.correlation_output)
if not os.path.exists(correlation_dir):
os.makedirs(correlation_dir)
self.writeFileHeader(self.correlation_output)
do_covariances = self.covariance_output is not None
if do_covariances:
if os.path.exists(self.covariance_output):
logging.info("%s already exists, delete it if you want it figured out again", self.covariance_output)
do_covariances = False
else:
covariance_dir = os.path.dirname(self.covariance_output)
if not os.path.exists(covariance_dir):
os.makedirs(covariance_dir)
self.writeFileHeader(self.covariance_output)
if not do_covariances and not do_correlations:
return
names = Utilities.dosageNamesFromFolder(self.data_folder)
for name in names:
snps, snps_by_rsid = self.getSNPS(name, weight_db_logic)
if do_correlations:
self.addToCorrelationFile(weight_db_logic, name, snps, snps_by_rsid)
if do_covariances:
self.addToCovarianceFile(weight_db_logic, name, snps, snps_by_rsid)
def buildFiles(self, weight_db_logic):
do_correlations = self.correlation_output is not None
if do_correlations:
if os.path.exists(self.correlation_output):
logging.info("%s already exists, delete it if you want it figured out again", self.correlation_output)
do_correlations = False
else:
correlation_dir = os.path.dirname(self.correlation_output)
if not os.path.exists(correlation_dir):
os.makedirs(correlation_dir)
self.writeFileHeader(self.correlation_output)
do_covariances = self.covariance_output is not None
if do_covariances:
if os.path.exists(self.covariance_output):
logging.info("%s already exists, delete it if you want it figured out again", self.covariance_output)
do_covariances = False
else:
covariance_dir = os.path.dirname(self.covariance_output)
if not os.path.exists(covariance_dir):
os.makedirs(covariance_dir)
self.writeFileHeader(self.covariance_output)
if not do_covariances and not do_correlations:
return
names = Utilities.dosageNamesFromFolder(self.data_folder)
for name in names:
snps, snps_by_rsid = self.getSNPS(name, weight_db_logic)
if do_correlations:
self.addToCorrelationFile(weight_db_logic, name, snps, snps_by_rsid)
if do_covariances:
self.addToCovarianceFile(weight_db_logic, name, snps, snps_by_rsid)
def run(self):
if os.path.exists(self.output_file):
logging.info("File %s already exists, delete it if you want it calculated again", self.output_file)
return
logging.info("Opening %s", self.weight_db)
weight_db_logic = WeightDBUtilities.WeightDBEntryLogic(self.db_path)
CHROMOSOMES = ["chr"+str(x) for x in xrange(1, 23)]
dosage_names = Utilities.dosageNamesFromFolder(self.data_folder_gwas_dosage)
legend_names = Utilities.legendNamesFromFolder(self.data_folder_phase)
findings={}
for chromosome in CHROMOSOMES:
logging.info("Processing chromosome %s", chromosome)
dosage_name = Utilities.removeNameWithPatterns(dosage_names, [chromosome+"."])
dosage = self.loadDosageFile(self.data_folder_gwas_dosage, dosage_name)
self.processDosage(chromosome, weight_db_logic, dosage, findings)
legend_name = Utilities.removeNameEndingWith(legend_names, chromosome)
self.processLegendName(chromosome, weight_db_logic, dosage, findings, legend_name)
with open(self.output_file, "w") as file:
file.write(AlleleStats.CSVHeader())
def sortByChromosome(finding):
return finding.chromosome
entries = sorted(findings.values(), key=sortByChromosome)
for finding in entries:
line = finding.toCSVLine()
file.write(line)
def testDosageNamesFromFolder(self):
names = Utilities.dosageNamesFromFolder("tests/_td/dosage_set_1")
self.assertEqual(names, [])
def testDosageNamesFromFolder(self):
names = Utilities.dosageNamesFromFolder("tests/_td/dosage_set_1")
self.assertEqual(names, [])
