def __init__(self, **keywords):
"""
"""
AbstractMapper.__init__(self, **keywords)
import re
self.numberGrabPattern = re.compile(r"^(\d+) \+ (\d+)")
def __init__(self, inputFnameLs=None, **keywords):
"""
2012.5.23
"""
AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
self.chromosomeList = utils.getListOutOfStr(self.chromosomeList,
data_type=str,
separator2=None)
self.chromosomeSet = set(self.chromosomeList)
self.fileFormatDict = {1: 'fasta', 2: 'fastq'}
if not self.inputFileFormat: #0 or None or ''
#use 1: to exclude the '.' in suffix
self.inputFileFormat = utils.getRealPrefixSuffixOfFilenameWithVariableSuffix(
self.inputFname)[1][1:]
else:
self.inputFileFormat = self.fileFormatDict.get(
self.inputFileFormat)
if not self.outputFileFormat: #0 or None or ''
self.outputFileFormat = utils.getRealPrefixSuffixOfFilenameWithVariableSuffix(
self.outputFname)[1][1:]
else:
self.outputFileFormat = self.fileFormatDict.get(
self.outputFileFormat)
def __init__(self, inputFnameLs, **keywords):
"""
2012.5.23
"""
AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
#self.blastnPath = self.insertHomePath(self.blastnPath, self.home_path)
self.blastallPath = self.insertHomePath(self.blastallPath,
self.home_path)
def __init__(self, **keywords):
"""
"""
AbstractMapper.__init__(self, **keywords)
self.convertFuncDict = {
1: self.convertMSOutput,
2: self.convertMSHOTLiteOutput
}
def __init__(self, inputFnameLs=None, **keywords): """ 2012.10.25 self.missingDataNotation will be processed into a set. """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords) #self.connectDB() called within its __init__() #if user wants to preserve data in a data structure that is visible throughout reading different files. # then use this self.invariantPData. self.invariantPData = PassingData(writer=None, headerOutputted=False, x_ls = [], y_ls = [], z_ls=[]) if getattr(self, 'missingDataNotation', None): self.missingDataNotation = set(utils.getListOutOfStr(self.missingDataNotation, data_type=str, separator2=None)) else: self.missingDataNotation = set()
def __init__(self, inputFnameLs=None, **keywords): """ """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs, **keywords): """ """ AbstractMapper.__init__(self, **keywords) self.inputFnameLs = inputFnameLs #2012.3.19 not used
def __init__(self, **keywords): """ """ AbstractMapper.__init__(self, **keywords)
def __init__(self, inputFnameLs, **keywords): """ 2012.8.19 """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs=None, **keywords):
AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, **keywords): """ """ AbstractMapper.__init__(self, **keywords) """
def __init__(self, inputFnameLs=None, **keywords):
"""
2011-7-12
"""
AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs, **keywords):
"""
"""
AbstractMapper.__init__(self, **keywords)
self.inputFnameLs = inputFnameLs #useless