예제 #1
0
    def __init__(self,
                 curs='',
                 input_fname1='',
                 input_fname2='',
                 latex_output_fname='',
                 accession2ecotype_table='',
                 diff_details_table='',
                 qc_cross_match_table='',
                 debug=0,
                 report=0):
        """
		2008-01-09
			add diff_details_table
		2008-01-11
			add qc_cross_match_table
		"""
        QualityControl.__init__(self, debug=0)
        self.curs = curs
        self.input_fname1 = input_fname1
        self.input_fname2 = input_fname2
        self.latex_output_fname = latex_output_fname
        self.accession2ecotype_table = accession2ecotype_table
        self.diff_details_table = diff_details_table
        self.qc_cross_match_table = qc_cross_match_table
        self.debug = int(debug)
        self.report = int(report)
예제 #2
0
 def __init__(self, curs="", input_fname1="", input_fname2="", latex_output_fname="", debug=0, report=0):
     QualityControl.__init__(self)
     self.curs = curs
     self.input_fname1 = input_fname1
     self.input_fname2 = input_fname2
     self.latex_output_fname = latex_output_fname
     self.debug = int(debug)
     self.report = int(report)
예제 #3
0
	def load_dstruc(self):
		if self.debug:
			import pdb
			pdb.set_trace()
		QualityControl.load_dstruc(self)
		from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
		FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
		self.header1, self.strain_acc_list1, self.category_list1, self.data_matrix1 = FilterStrainSNPMatrix_instance.read_data(self.input_fname1)
		self.header2, self.strain_acc_list2, self.category_list2, self.data_matrix2 = FilterStrainSNPMatrix_instance.read_data(self.input_fname2)
	 	
		self.col_id2col_index1, self.col_id2col_index2, self.col_id12col_id2 = self.get_col_matching_dstruc(self.header1, self.header2, self.curs, self.snp_locus_table_250k, self.snp_locus_table_149snp)
		self.row_id2row_index1, self.row_id2row_index2, self.row_id12row_id2 = self.get_row_matching_dstruc(self.strain_acc_list1, self.category_list1, self.strain_acc_list2, self.curs, self.ecotype_duplicate2tg_ecotypeid_table)
예제 #4
0
 def __init__(self,
              curs='',
              input_fname1='',
              input_fname2='',
              latex_output_fname='',
              debug=0,
              report=0):
     QualityControl.__init__(self)
     self.curs = curs
     self.input_fname1 = input_fname1
     self.input_fname2 = input_fname2
     self.latex_output_fname = latex_output_fname
     self.debug = int(debug)
     self.report = int(report)
예제 #5
0
    def load_dstruc(self):
        if self.debug:
            import pdb
            pdb.set_trace()
        QualityControl.load_dstruc(self)
        from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
        FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
        self.header1, self.strain_acc_list1, self.category_list1, self.data_matrix1 = self.readTina2010In250kSNPs(
            self.input_fname1)
        self.header2, self.strain_acc_list2, self.category_list2, self.data_matrix2 = FilterStrainSNPMatrix_instance.read_data(
            self.input_fname2)

        self.col_id2col_index1, self.col_id2col_index2, self.col_id12col_id2 = self.get_col_matching_dstruc(
            self.header1, self.header2)
        self.row_id2row_index1, self.row_id2row_index2, self.row_id12row_id2 = self.get_row_matching_dstruc(
            self.curs, self.strain_acc_list1, self.strain_acc_list2)
예제 #6
0
	def __init__(self, curs='', input_fname1='', input_fname2='', latex_output_fname='', accession2ecotype_table='', diff_details_table='', qc_cross_match_table='', debug=0, report=0):
		"""
		2008-01-09
			add diff_details_table
		2008-01-11
			add qc_cross_match_table
		"""
		QualityControl.__init__(self, debug=0)
		self.curs = curs
		self.input_fname1 = input_fname1
		self.input_fname2 = input_fname2
		self.latex_output_fname = latex_output_fname
		self.accession2ecotype_table = accession2ecotype_table
		self.diff_details_table = diff_details_table
		self.qc_cross_match_table = qc_cross_match_table
		self.debug = int(debug)
		self.report = int(report)
    def get_row_matching_dstruc(self, strain_acc_list1, category_list1,
                                strain_acc_list2):
        """
		2008-05-06
		"""
        return QualityControl.get_row_matching_dstruc(strain_acc_list1,
                                                      category_list1,
                                                      strain_acc_list2)
예제 #8
0
    def load_dstruc(self):
        if self.debug:
            import pdb
            pdb.set_trace()
        QualityControl.load_dstruc(self)
        from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
        FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
        self.header1, self.strain_acc_list1, self.category_list1, self.data_matrix1 = FilterStrainSNPMatrix_instance.read_data(
            self.input_fname1)
        self.header2, self.strain_acc_list2, self.category_list2, self.data_matrix2 = FilterStrainSNPMatrix_instance.read_data(
            self.input_fname2)

        self.col_id2col_index1, self.col_id2col_index2, self.col_id12col_id2 = self.get_col_matching_dstruc(
            self.header1, self.header2, self.curs, self.snp_locus_table_250k,
            self.snp_locus_table_149snp)
        self.row_id2row_index1, self.row_id2row_index2, self.row_id12row_id2 = self.get_row_matching_dstruc(
            self.strain_acc_list1, self.category_list1, self.strain_acc_list2,
            self.curs, self.ecotype_duplicate2tg_ecotypeid_table)
예제 #9
0
    def load_dstruc(self):
        if self.debug:
            import pdb

            pdb.set_trace()
        QualityControl.load_dstruc(self)
        from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix

        FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
        self.header1, self.strain_acc_list1, self.category_list1, self.data_matrix1 = self.readTina2010In250kSNPs(
            self.input_fname1
        )
        self.header2, self.strain_acc_list2, self.category_list2, self.data_matrix2 = FilterStrainSNPMatrix_instance.read_data(
            self.input_fname2
        )

        self.col_id2col_index1, self.col_id2col_index2, self.col_id12col_id2 = self.get_col_matching_dstruc(
            self.header1, self.header2
        )
        self.row_id2row_index1, self.row_id2row_index2, self.row_id12row_id2 = self.get_row_matching_dstruc(
            self.curs, self.strain_acc_list1, self.strain_acc_list2
        )
예제 #10
0
	def get_row_matching_dstruc(self, strain_acc_list1, category_list1, strain_acc_list2):
		"""
		2008-05-06
		"""
		return QualityControl.get_row_matching_dstruc(strain_acc_list1, category_list1, strain_acc_list2)