def __init__(self, **keywords): """ 2009-4-10 simplified further by moving db-common lines to ElixirDB 2008-07-31 """ 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):
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):
"""
2012.9.5 set default minDepth=0
2011-9-27
"""
self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
self.header = None #2012.5.10 the list of column headers (the header line starting by #CHROM)
self.headerWithoutHash = None #2012.5.10 same as self.header except, instead of "#CHROM", it is "CHROM".
self.sample_id_ls = []
self.sample_id2index = {} #the index is the index of its column in the genotype_call_matrix
self.locus_id_ls = []
self.locus_id2row_index = {}
self.locus_id2data = {}
self.genotype_call_matrix = []
self.col_name2index = {} #column index in file
self.col_index_individual_name_ls = None
self.individual_name2col_index = {} #not the matrix column, the column in input file
self.metaInfoLs = [] #2012.3.28 anything before the "#CHROM" line. each entry is a raw line content, including '\n'
self.sampleIDHeader = [] #2012.3.20 a list of sample column headers (from sampleStartingColumn)
self.inf = None
self.reader = None
self._initializeInput(self.inputFname)
self.outf = None
self.writer = None
self._initializeOutput(self.outputFname)
def __init__(self, inputFname=None, **keywords):
self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
if not self.inputFname:
self.inputFname = inputFname
self.header = None
self.combinedColIDList = None #same as header
self.combinedColID2ColIndex = None
self.hdf5File = h5py.File(self.inputFname, self.openMode)
self.tableObjectList = []
self.tablePath2Index = {}
if self.openMode=='r':
self._readInData()
elif self.openMode=='w':
self.createNewTable(tableName=self.tableName, dtype=self.dtype, rowDefinition=self.rowDefinition)
self.rowIndexCursor = 0 #2012.11.16 for iteration
def __init__(self, **keywords):
"""
dataMatrixDtype could be a compound type:
http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html
http://docs.scipy.org/doc/numpy/reference/generated/numpy.dtype.html
#A record data type containing a 16-character string (in field name)
#and a sub-array of two 64-bit floating-point number (in field grades):
dt = numpy.dtype([('name', numpy.str_, 16), ('grades', numpy.float64, (2,))])
my_dtype = numpy.dtype([('field1', 'i'), ('field2', 'f'), ('field3', varLenStrType)])
#Using array-protocol type strings:
#each number below is counting bytes, not bits
>>> numpy.dtype([('a','f8'),('b','S10')])
dtype([('a', '<f8'), ('b', '|S10')])
#Using tuples. int is a fixed type, 3 the field's shape. void is a flexible type, here of size 10:
numpy.dtype([('hello',(numpy.int,3)),('world',numpy.void,10)])
#Using dictionaries. Two fields named 'gender' and 'age':
numpy.dtype({'names':['gender','age'], 'formats':['S1',numpy.uint8]})
#Offsets in bytes, here 0 and 25:
numpy.dtype({'surname':('S25',0),'age':(numpy.uint8,25)})
"""
self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
self.dataMatrixDSName = "dataMatrix"
self.rowIDListDSName = "rowIDList"
self.colIDListDSName = "colIDList"
if not self.newGroup:
self._readInData()
else:
self._createDatasetSkeletonForOneGroup(h5Group=self.h5Group, dtype=self.dataMatrixDtype)
self.newWrite = True #a flag used to control whether it's first time to write stuff (first time=set whole matrix)
self.rowIndexCursor = 0
def __init__(self, inputFname=None, **keywords): self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \ class_to_have_attr=self) if not self.inputFname: self.inputFname = inputFname if self.inputFname and self.inputFile is None: self.inputFile = utils.openGzipFile(self.inputFname, openMode=self.openMode) self.filename = self.inputFname #2013.05.03 for easy access self.csvFile = None self.isRealCSV = False if self.openMode=='r': #reading mode if self.delimiter is None: self.delimiter = figureOutDelimiter(self.inputFile) if self.delimiter=='\t' or self.delimiter==',': self.csvFile = csv.reader(self.inputFile, delimiter=self.delimiter) self.isRealCSV = True else: self.csvFile = self.inputFile self.isRealCSV = False else: #writing mode if not self.delimiter: self.delimiter = '\t' self.csvFile = csv.writer(self.inputFile, delimiter=self.delimiter) self.isRealCSV = True #else: # self.csvFile = self.inputFile # self.isRealCSV = False self.col_name2index = None self._row = None #2013.08.30 to store the current row being read self.headerPattern = re.compile(r'^[a-zA-Z]') #default header pattern, line beginned with letter self.commentPattern = re.compile(r'^#') #default, beginned with # self.comment_row_list = []
nonFounderIndividualIDSet=nonFounderIndividualIDSet)
def _reportFamilyStructure(self, noOfParents2FamilyData=None):
"""
2013.07.19
"""
sys.stderr.write("\t%s\t%s\t%s\t%s\t%s\n"%("parentSetSize", "noOfFamilies", "noOfParents", "noOfKids", "noOfUniqueIndividuals"))
for noOfParents, familyData in noOfParents2FamilyData.iteritems():
parentIDSet = familyData.parentIDSet
childIDSet = familyData.childIDSet
individualIDSet = familyData.individualIDSet
sys.stderr.write("\t%s\t%s\t%s\t%s\t%s\n"%(noOfParents, len(familyData.parentTupleSet), len(parentIDSet), \
len(childIDSet), len(individualIDSet)))
def next(self):
try:
row = self.csvFile.next()
except:
raise StopIteration
if not self.isRealCSV:
row = row.strip().split()
familyID, individualID, paternalID, maternalID, sex, phenotype = row
return PassingData(familyID=familyID, individualID=individualID, paternalID=paternalID, \
maternalID=maternalID, sex=sex, phenotype=phenotype)
if __name__ == '__main__':
main_class = PlinkPedigreeFile
po = ProcessOptions(sys.argv, main_class.option_default_dict, error_doc=main_class.__doc__)
instance = main_class(**po.long_option2value)
instance.run()