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 __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)
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 __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)
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 __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)
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 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 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)