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)
