Python Utilities.dosageName Examples

Example #1

File: single_tissue_covariance.py Project: pythseq/UTMOST

 def getSNPS(self, name, weight_db_logic):
     dosageLoader = None
     if self.input_format == Formats.IMPUTE:
         dosageLoader = ThousandGenomesUtilities.IMPUTEDosageLoader(self.data_folder, name) #outdated code
     elif self.input_format == Formats.PrediXcan:
         dosageName = Utilities.dosageName(name)
         path = os.path.join(self.data_folder, dosageName)
         dosageLoader = PrediXcanFormatUtilities.PrediXcanFormatDosageLoader(path, weight_db_logic)
     else:
         logging.info("Invalid input format: %s", self.input_format)
         return
     snps, snps_by_rsid = dosageLoader.load()
     return snps, snps_by_rsid

Example #2

File: M01_covariances_correlations.py Project: Varoona/MetaXcan

 def getSNPS(self, name, weight_db_logic):
     dosageLoader = None
     if self.input_format == Formats.IMPUTE:
         dosageLoader = ThousandGenomesUtilities.IMPUTEDosageLoader(self.data_folder, name) #outdated code
     elif self.input_format == Formats.PrediXcan:
         dosageName = Utilities.dosageName(name)
         path = os.path.join(self.data_folder, dosageName)
         dosageLoader = PrediXcanFormatUtilities.PrediXcanFormatDosageLoader(path, weight_db_logic)
     else:
         logging.info("Invalid input format: %s", self.input_format)
         return
     snps, snps_by_rsid = dosageLoader.load()
     return snps, snps_by_rsid

Example #3

 def testDosageName(self):
     dosage_name = Utilities.dosageName("a")
     self.assertEqual(dosage_name, "a.dosage.gz")

Example #4

File: test_utilities.py Project: Varoona/MetaXcan

 def testDosageName(self):
     dosage_name = Utilities.dosageName("a")
     self.assertEqual(dosage_name, "a.dosage.gz")