def __init__(self,conifer_file=None,samples = None): """A ConiferPipeline is designed to segment and call CNVs from a CoNIFER analysis file""" if conifer_file is not None: self.h5file = conifer_file # TODO test if valid file try: self.r = rpkm.rpkm_reader(self.h5file) except: print "Error in reading or opening HDF5 analysis file" return None # get contig names self.contigs = self.r.getContigList() # get sample names if samples == None: self.samples = self.r.getSampleList() else: self.samples = samples else: pass rpy2.rinterface.set_writeconsole(self.Rlog) self.stderr_log = "" self.stdout_log = "" self.log_level = 0
def __init__(self, conifer_file): try: _ = locale.setlocale(locale.LC_ALL, '') except: print "Warning: Could not set locale" if conifer_file is not None: self.h5file = conifer_file # TODO test if valid file try: self.r = rpkm.rpkm_reader(self.h5file) except: print "Error in reading or opening HDF5 analysis file" return None # get contig names self.contigs = self.r.getContigList() # get sample names self.samples = self.r.getSampleList() # set up empty track list self.tracks = [] else: pass