def __init__(self,
path,
accessor,
sense_specific=True,
description="unlabeled track",
system="hg18",
dim=1,
auto_flush=False,
mode="r",
**kwargs):
self.path = path
self.mode = mode
self.acc_cache = {}
self.accessor = accessor
self.kwargs = kwargs
self.sense_specific = to_bool(sense_specific)
self.dim = int(dim)
self.description = description
self.auto_flush = auto_flush
self.last_chrom = ""
self.logger = getLogger("Track('%s')" % path)
self.system = system
self.logger.debug("Track(auto_flush=%s)" % (str(auto_flush)))
kwargs['sense_specific'] = self.sense_specific
kwargs['mode'] = self.mode
kwargs['system'] = self.system
kwargs['description'] = self.description
kwargs['dim'] = self.dim
if "w" in mode:
# make sure the path exists right away so that the accessors
# can flush the actual data there!
from byo.io import ensure_path
ensure_path(self.path)
def __init__(self,path,accessor,sense_specific=True,description="unlabeled track",system=None,dim=1,auto_flush=False,mode="r",**kwargs):
self.path = path
self.mode = mode
self.acc_cache = {}
self.accessor = accessor
self.kwargs = kwargs
self.sense_specific = to_bool(sense_specific)
self.dim = int(dim)
self.description = description
self.auto_flush = auto_flush
self.last_chrom = ""
self.logger = logging.getLogger("byo.Track({0} {1} '{2}')".format(system,accessor,path))
self.system = system
self.no_data = False
self.logger.debug("Track(auto_flush=%s)" % (str(auto_flush)))
kwargs['sense_specific'] = self.sense_specific
kwargs['mode'] = self.mode
kwargs['system'] = self.system
kwargs['description'] = self.description
kwargs['dim'] = self.dim
if "w" in mode:
# make sure the path exists right away so that the accessors
# can flush the actual data there!
from byo.io import ensure_path
ensure_path(self.path)
def __init__(self,path,chrom,sense,sense_specific=True,dtype=numpy.float32,mode="r",dim=1,ext=".bin",**kwargs):
super(ArrayAccessor,self).__init__(path,chrom,sense,sense_specific=sense_specific,**kwargs)
self.logger = logging.getLogger('byo.io.ArrayAccessor')
self.logger.debug("mmap'ing '%s' array data for chromosome %s%s from '%s'" % (str(dtype),chrom,sense,path))
# in case we havent been given the actual type, just its name: retrieve it
if type(dtype) == str:
dtype = getattr(numpy,dtype)
self.dtype=dtype
self.sense_specific = sense_specific
self.dim = dim
# preferred mode-codes for how to open an mmap array by assumed intention
mode_trans = {"r" : "c","rw":"w+","w":"w+"}
if sense_specific:
fname = os.path.join(path,chrom+sense+ext)
else:
fname = os.path.join(path,chrom+ext)
if not "w" in mode:
# read-only access
try:
self.data = numpy.memmap(filename=fname,dtype=dtype,mode=mode_trans[mode])
except IOError:
self.logger.warning("Could not access '%s'. Switching to dummy mode (only zeros)" % fname)
self.data = ZeroSource(self.dtype)
#self.get_data = self.get_dummy
else:
# create a sparse file
from byo.io import ensure_path
ensure_path(path)
import byo.systems
system = getattr(byo.systems,kwargs['system'])
try:
size = system.chr_sizes[chrom]
except KeyError:
self.logger.warning("Unknown chromosome '%s'. Switching to (read-only) dummy mode (only zeros)" % fname)
self.data = ZeroSource(self.dtype)
else:
self.logger.info("opening '%s' (size=%d) for write-access" % (fname,size))
self.data = numpy.memmap(filename=fname,dtype=dtype,mode=mode_trans[mode],shape=size)
def __init__(self,path,chrom,sense,sense_specific=True,dtype=numpy.float32,mode="r",dim=1,**kwargs):
debug("# ArrayAccessor mmap: Loading '%s' array data for chromosome %s%s from '%s'" % (str(dtype),chrom,sense,path))
super(ArrayAccessor,self).__init__(path,chrom,sense,sense_specific=sense_specific,**kwargs)
# in case we havent been given the actual type, just its name: retrieve it
if type(dtype) == str:
dtype = getattr(numpy,dtype)
self.dtype=dtype
self.sense_specific = sense_specific
self.dim = dim
# preferred mode-codes for how to open an mmap array by assumed intention
mode_trans = {"r" : "c","rw":"w+","w":"w+"}
if sense_specific:
fname = os.path.join(path,chrom+sense+".bin")
else:
fname = os.path.join(path,chrom+".bin")
if not "w" in mode:
# read-only access
try:
self.data = numpy.memmap(filename=fname,dtype=dtype,mode=mode_trans[mode])
except IOError:
warning("Could not access '%s'. Switching to dummy mode (only zeros)" % fname)
self.data = ZeroSource(self.dtype)
#self.get_data = self.get_dummy
else:
# create a sparse file
from byo.io import ensure_path
ensure_path(path)
import byo.systems
system = getattr(byo.systems,kwargs['system'])
try:
size = system.chr_sizes[chrom]
except KeyError:
warning("Unknown chromosome '%s'. Switching to (read-only) dummy mode (only zeros)" % fname)
self.data = ZeroSource(self.dtype)
else:
info("opening '%s' (size=%d) for write-access" % (fname,size))
self.data = numpy.memmap(filename=fname,dtype=dtype,mode=mode_trans[mode],shape=size)
def prep_storage(self):
from byo.io import ensure_path
import os
if not self.store:
ensure_path(os.path.dirname(self.path))
self.store = file(self.path, "w")
def prep_storage(self):
from byo.io import ensure_path
import os
if not self.store:
ensure_path(os.path.dirname(self.path))
self.store = file(self.path,"w")