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
