def run(self): """ 2008-08-11 the database interface changed in variation.src.dbsnp 2008-05-06 """ import MySQLdb conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user=self.user, passwd=self.passwd) curs = conn.cursor() if self.debug: import pdb pdb.set_trace() db = DBSNP(username=self.user, password=self.passwd, hostname=self.hostname, database=self.dbname) session = db.session session.begin() #transaction = session.create_transaction() snps_name2possible_mappings, snps_name2snps_id = self.get_snps_name2possible_mappings( db) from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data( self.input_fname1) snpData1 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix, \ col_id2id=snps_name2snps_id, snps_table='dbsnp.snps') header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data( self.input_fname2) snpData2 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix,\ snps_table='stock_250k.snps') twoSNPData = TwoSNPData384(SNPData1=snpData1, SNPData2=snpData2, curs=curs, user=self.user) readme = formReadmeObj(sys.argv, self.ad, README) session.save(readme) session.flush() twoSNPData.figureOutABMapping(session, readme, snps_name2possible_mappings) if self.commit: curs.execute("commit") session.commit() else: session.rollback()
def run(self): """ 2008-08-11 the database interface changed in variation.src.dbsnp 2008-05-06 """ import MySQLdb conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user = self.user, passwd = self.passwd) curs = conn.cursor() if self.debug: import pdb pdb.set_trace() db = DBSNP(username=self.user, password=self.passwd, hostname=self.hostname, database=self.dbname) session = db.session session.begin() #transaction = session.create_transaction() snps_name2possible_mappings, snps_name2snps_id = self.get_snps_name2possible_mappings(db) from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data(self.input_fname1) snpData1 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix, \ col_id2id=snps_name2snps_id, snps_table='dbsnp.snps') header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix.read_data(self.input_fname2) snpData2 = SNPData(header=header, strain_acc_list=strain_acc_list, category_list=category_list, data_matrix=data_matrix,\ snps_table='stock_250k.snps') twoSNPData = TwoSNPData384(SNPData1=snpData1, SNPData2=snpData2, curs=curs, user=self.user) readme = formReadmeObj(sys.argv, self.ad, README) session.save(readme) session.flush() twoSNPData.figureOutABMapping(session, readme, snps_name2possible_mappings) if self.commit: curs.execute("commit") session.commit() else: session.rollback()
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)
def read_2010_x_149SNP(input_fname): """ 2007-12-30 """ from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix() header, strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(input_fname) snp_acc_ls = header[2:] snp_acc2col_index = dict(zip(snp_acc_ls, range(len(snp_acc_ls)))) accession_id_ls = map(int, strain_acc_list) accession_id2row_index = dict(zip(accession_id_ls, range(len(accession_id_ls)))) return snp_acc2col_index, accession_id2row_index, data_matrix
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)
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 )
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)