コード例 #1
0
    def __init__(self, **keywords):
        """
		2008-11-10
		"""
        ProcessOptions.process_function_arguments(
            keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self
        )
        if self.phenotype_method_id_ls:
            self.phenotype_method_id_ls = getListOutOfStr(self.phenotype_method_id_ls, data_type=int)

        self.which_PC_index_ls = getListOutOfStr(self.which_PC_index_ls, data_type=int)

        self.run_whole_matrix = {
            1: self._kruskal_wallis_whole_matrix,
            2: self.LM_whole_matrix,
            3: self.Emma_whole_matrix,
            4: self.LM_with_PCs_whole_matrix,
            5: self.LM_with_PCs_whole_matrix,
            6: self.LM_with_PCs_whole_matrix,
            7: self.Emma_whole_matrixForNoNAGenotypeMatrix,
            8: self.EMMAX,
        }

        self.output_results = {
            1: self.output_kw_results,
            2: self.output_lm_results,
            3: self.output_lm_results,
            7: self.output_emma_results,
        }
コード例 #2
0
	def __init__(self, **keywords):
		"""
		2009-4-18
		"""
		
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #3
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ファイル: JobDB.py プロジェクト: polyactis/utility
	def __init__(self, **keywords):
		"""
		2008-10-29
			database to control cluster jobs
		"""
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		self.setup_engine(metadata=__metadata__, session=__session__, entities=entities)
コード例 #4
0
ファイル: GenomeDatabase.py プロジェクト: polyactis/transfac
	def __init__(self, **keywords):
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		
		self._threadlocal = threading.local()
		self.tables = {}
		self.mappers = {}
		self._engine = None
コード例 #5
0
	def __init__(self, **keywords):
		"""
		2008-10-23
			simplified, relegate stuff to ElixirDB
		2008-07-09
		"""
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		self.setup_engine(metadata=__metadata__, session=__session__, entities=entities)
コード例 #6
0
	def __init__(self, **keywords):
		"""
		2008-04-28
			use ProcessOptions, newer option handling class
		2008-04-16
		"""
		
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #7
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	def __init__(self, **keywords):
		"""
		2008-06-02
			use ProcessOptions
		2007-07-11
		2007-07-13
			input_fname is useless
		"""
		
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #8
0
	def __init__(self,  **keywords):
		"""
		2008-06-02
			use ProcessOptions
		2007-07-16
		"""
		
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		
		cutoff_ls = self.max_row_NA_max_col_NA_min_log_prob.split(',')
		self.row_cutoff, self.col_cutoff, self.min_log_prob = map(float, cutoff_ls)
コード例 #9
0
    def __init__(self, **keywords):
        """
		2009-4-10
			simplified further by moving db-common lines to ElixirDB
		2008-08-11
		"""
        from pymodule.ProcessOptions import ProcessOptions

        ProcessOptions.process_function_arguments(
            keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self
        )
        self.setup_engine(metadata=__metadata__, session=__session__, entities=entities)
コード例 #10
0
    def __init__(self, **keywords):
        """
		2008-05-01
			use ProcessOptions
		"""
        from pymodule import ProcessOptions

        ProcessOptions.process_function_arguments(
            keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self
        )
        if not self.output_fname:
            self.output_fname = "%s_w%s.npute" % (self.input_fname, self.single_window_size)
コード例 #11
0
	def __init__(self, **keywords):
		"""
		2008-12-02
			modelled after ConvertYuSNPFormat2Bjarni.py
		"""
		from pymodule import ProcessOptions
		self.ad=ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #12
0
	def __init__(self,  **keywords):
		"""
		2011-7-12
		"""
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
														class_to_have_attr=self)
		self.discoverFuncDict = {1: self.discoverFromVCF, 2: self.discoverFromBAM, 3:self.discoverFromVCFWithoutFilter}
コード例 #13
0
	def __init__(self, **keywords):
		"""
		2008-05-27
			add user & password
		2007-12-29
			add processing_bits
		"""
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		
		processing_bits = self.processing_bits
		self.processing_bits = [0]*len(processing_bits)
		for i in range(len(processing_bits)):
			self.processing_bits[i] = int(processing_bits[i])
		
		self.data_type2data_table = {0:'at.locus',
									1:'chip.snp_combined_may_9_06_no_van'}
コード例 #14
0
	def __init__(self,  **keywords):
		"""
		2008-09-05
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		self.call_method_id_ls = getListOutOfStr(self.call_method_id_ls, data_type=int)
コード例 #15
0
	def __init__(self, inputFnameLs, **keywords):
		"""
		2011-7-11
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
														class_to_have_attr=self)
コード例 #16
0
	def __init__(self, **keywords):
		"""
		2008-09-29
			add option min_LD_to_output and min_MAF
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #17
0
	def __init__(self, refNameLs, **keywords):
		"""
		2011-7-11
		"""
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
														class_to_have_attr=self)
		self.refNameLs = refNameLs
コード例 #18
0
	def __init__(self, **keywords):
		"""
		2008-04-08
		"""
		from pymodule import ProcessOptions
		self.ad=ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		if self.array_id_ls:
			self.array_id_ls = getListOutOfStr(self.array_id_ls, data_type=str)
コード例 #19
0
	def __init__(self, **keywords):
		"""
		2008-4-4
		"""
		#argument dictionary
		#self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=__doc__, class_to_have_attr=self)
		from pymodule import ProcessOptions
		self.ad=ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #20
0
	def __init__(self, **keywords):
		"""
		2008-05-11
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		if self.ecotype_id_ls:
			self.ecotype_id_ls = getListOutOfStr(self.ecotype_id_ls, data_type=str)	#str because ecotype ids in SNPData are not converted to integers
コード例 #21
0
	def __init__(self,  **keywords):
		"""
		2008-10-19
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		if self.output_dir and not os.path.isdir(self.output_dir):
			os.makedirs(self.output_dir)
コード例 #22
0
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		"""
		AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		
		listArgumentName_data_type_ls = [("site_id_ls", int), ('country_id_ls', int), ('tax_id_ls', int)]
		listArgumentName2hasContent = ProcessOptions.processListArguments(listArgumentName_data_type_ls,\
												emptyContent=[], class_to_have_attr=self)
コード例 #23
0
	def __init__(self, **keywords):
		"""
		2008-05-18
			add argument array_id_2nd_column
		2008-5-12
		"""
		from pymodule import ProcessOptions
		self.ad=ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #24
0
	def __init__(self, **keywords):
		"""
		2008-06-02
			use ProcessOptions
		2007-07-13
			add output_type, need_heterozygous_call, with_header_line, nt_alphabet
		2007-07-16
			change snpacc_fname to popid2snpid_table
		2007-07-16
		"""
		
		from pymodule import ProcessOptions
		ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)		
		
		self.OutputPop_dict = {1: self.OutputPopMatrixFormat,
			2: self.OutputPopRMES,
			3: self.OutputPopMIH}
コード例 #25
0
	def __init__(self,  **keywords):
		"""
		2008-07-24
			split results_method_id_ls if it exists, to accomodate MpiGeneListRankTest which removed this option
		2008-07-10
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
コード例 #26
0
	def __init__(self,  **keywords):
		"""
		2008-11-14
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		self.pic_area =  self.pic_area.split(',')
		self.pic_area = map(int, self.pic_area)
コード例 #27
0
	def __init__(self, **keywords):
		"""
		2008-05-13
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		plot_func_dict = {1:PlotQCCall._plot3D,\
						2:PlotQCCall._plotContour}
		self._plot = plot_func_dict[self.plot_type]
コード例 #28
0
	def __init__(self,  **keywords):
		"""
		2011-7-11
		"""
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
														class_to_have_attr=self)
		
		if not self.outputFnamePrefix:
			self.outputFnamePrefix = utils.getRealPrefixSuffixOfFilenameWithVariableSuffix(self.inputFname)[0]
コード例 #29
0
	def __init__(self, inputFnameLs, **keywords):
		"""
		2011-10-19
		This class is the entry to all others.
		"""
		from pymodule import ProcessOptions
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
		
		self.inputFnameLs = inputFnameLs
コード例 #30
0
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		2011-7-12
		"""
		self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
														class_to_have_attr=self)
		self.originalHeaderLength = 0
		self.originalHeader = None
		self.col_name2index = {}