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,
}
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)
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)
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
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)
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)
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)
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)
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)
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)
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)
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}
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'}
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)
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)
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)
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
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)
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)
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
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)
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)
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)
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}
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)
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)
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]
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]
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
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 = {}
