def load_chromosome(in_f, fast=2):
"""
Load a Chromosome object from a file. A Chromosome object can be saved with
the :func:`Chromosome.save_chromosome` function.
:param in_f: path to a saved Chromosome object file
:param 2 fast: if fast=2 do not load the Hi-C data (in the case that they
were saved in a separate file see :func:`Chromosome.save_chromosome`).
If fast is equal to 1, the weights will be skipped from load to save
memory. Finally if fast=0, both the weights and Hi-C data will be loaded
:returns: a Chromosome object
TODO: remove first try/except type error... this is loading old experiments
"""
dico = load(open(in_f))
name = ''
crm = Chromosome(dico['name'])
for name in dico['experiments']:
xpr = Experiment(name, dico['experiments'][name]['resolution'],
no_warn=True)
xpr.tads = dico['experiments'][name]['tads']
xpr.norm = dico['experiments'][name]['wght']
xpr.hic_data = dico['experiments'][name]['hi-c']
xpr.conditions = dico['experiments'][name]['cond']
xpr.size = dico['experiments'][name]['size']
try:
crm.experiments.append(xpr)
except TypeError:
continue
crm.size = dico['size']
crm.r_size = dico['r_size']
crm.max_tad_size = dico['max_tad_size']
crm.forbidden = dico['forbidden']
crm._centromere = dico['_centromere']
if type(dico['experiments'][name]['hi-c']) == str and fast!= int(2):
try:
dicp = load(open(in_f + '_hic'))
except IOError:
raise Exception('ERROR: file %s not found\n' % (
dico['experiments'][name]['hi-c']))
for name in dico['experiments']:
crm.get_experiment(name).hic_data = dicp[name]['hi-c']
if fast != 1:
crm.get_experiment(name).norm = dicp[name]['wght']
elif not fast:
warn('WARNING: data not saved correctly for fast loading.\n')
return crm
def load_chromosome(in_f, fast=2):
"""
Load Chromosome from file. Chromosome might have been saved through the
:func:`Chromosome.save_chromosome`.
:param in_f: path to a saved Chromosome file
:param 2 fast: if fast=2 do not load Hi-C data (in the case that they were
saved in a separate file see :func:`Chromosome.save_chromosome`). If fast
is equal to 1, weight would be skipped from load in order to save memory.
Finally if fast=0, both weights and Hi-C data will be loaded.
:returns: Chromosome object
TODO: remove first try/except type error... this is loading old experiments
"""
dico = load(open(in_f))
name = ""
crm = Chromosome(dico["name"])
for name in dico["experiments"]:
xpr = Experiment(name, dico["experiments"][name]["resolution"], no_warn=True)
xpr.tads = dico["experiments"][name]["tads"]
xpr.wght = dico["experiments"][name]["wght"]
xpr.hic_data = dico["experiments"][name]["hi-c"]
xpr.conditions = dico["experiments"][name]["cond"]
xpr.size = dico["experiments"][name]["size"]
try:
crm.experiments.append(xpr)
except TypeError:
continue
crm.size = dico["size"]
crm.r_size = dico["r_size"]
crm.max_tad_size = dico["max_tad_size"]
crm.forbidden = dico["forbidden"]
crm._centromere = dico["_centromere"]
if type(dico["experiments"][name]["hi-c"]) == str and fast != int(2):
try:
dicp = load(open(in_f + "_hic"))
except IOError:
raise Exception("ERROR: file {} not found\n".format(dico["experiments"][name]["hi-c"]))
for name in dico["experiments"]:
crm.get_experiment(name).hic_data = dicp[name]["hi-c"]
if fast != 1:
crm.get_experiment(name).wght = dicp[name]["wght"]
elif not fast:
warn("WARNING: data not saved correctly for fast loading.\n")
return crm
def load_chromosome(in_f, fast=2):
"""
Load a Chromosome object from a file. A Chromosome object can be saved with
the :func:`Chromosome.save_chromosome` function.
:param in_f: path to a saved Chromosome object file
:param 2 fast: if fast=2 do not load the Hi-C data (in the case that they
were saved in a separate file see :func:`Chromosome.save_chromosome`).
If fast is equal to 1, the weights will be skipped from load to save
memory. Finally if fast=0, both the weights and Hi-C data will be loaded
:returns: a Chromosome object
TODO: remove first try/except type error... this is loading old experiments
"""
dico = load(open(in_f))
name = ''
crm = Chromosome(dico['name'])
try:
exp_order = dico['experiment_order']
except KeyError:
exp_order = dico['experiments'].keys()
for name in exp_order:
xpr = Experiment(name, dico['experiments'][name]['resolution'],
no_warn=True)
xpr.tads = dico['experiments'][name]['tads']
xpr.norm = dico['experiments'][name]['wght']
xpr.hic_data = dico['experiments'][name]['hi-c']
xpr.conditions = dico['experiments'][name]['cond']
xpr.size = dico['experiments'][name]['size']
xpr._zeros = dico['experiments'][name].get('zero', {})
try: # new in version post-CSDM13
xpr.identifier = dico['experiments'][name]['iden']
xpr.cell_type = dico['experiments'][name]['cell']
xpr.exp_type = dico['experiments'][name]['expt']
xpr.enzyme = dico['experiments'][name]['enzy']
xpr.description = dico['experiments'][name]['desc']
except KeyError:
xpr.identifier = None
xpr.cell_type = None
xpr.exp_type = None
xpr.enzyme = None
xpr.description = {}
try:
crm.experiments.append(xpr)
except TypeError:
continue
crm.size = dico['size']
crm.r_size = dico['r_size']
crm.max_tad_size = dico['max_tad_size']
crm.forbidden = dico['forbidden']
crm._centromere = dico['_centromere']
try: # new in version post-CSDM13
crm.species = dico['species']
crm.assembly = dico['assembly']
crm.description = dico['description']
except KeyError:
crm.species = None
crm.assembly = None
crm.description = {}
if isinstance(dico['experiments'][name]['hi-c'], str) or fast != int(2):
try:
dicp = load(open(in_f + '_hic'))
except IOError:
raise Exception('ERROR: file %s not found\n' % (
dico['experiments'][name]['hi-c']))
for name in dico['experiments']:
crm.get_experiment(name).hic_data = dicp[name]['hi-c']
if fast != 1:
crm.get_experiment(name).norm = dicp[name]['wght']
elif not fast:
stderr.write('WARNING: data not saved correctly for fast loading.\n')
return crm
def load_chromosome(in_f, fast=2):
"""
Load a Chromosome object from a file. A Chromosome object can be saved with
the :func:`Chromosome.save_chromosome` function.
:param in_f: path to a saved Chromosome object file
:param 2 fast: if fast=2 do not load the Hi-C data (in the case that they
were saved in a separate file see :func:`Chromosome.save_chromosome`).
If fast is equal to 1, the weights will be skipped from load to save
memory. Finally if fast=0, both the weights and Hi-C data will be loaded
:returns: a Chromosome object
TODO: remove first try/except type error... this is loading old experiments
"""
with open(in_f,'rb') as f_in_f:
dico = load(f_in_f)
name = ''
crm = Chromosome(dico['name'])
try:
exp_order = dico['experiment_order']
except KeyError:
exp_order = list(dico['experiments'].keys())
for name in exp_order:
xpr = Experiment(name, dico['experiments'][name]['resolution'],
no_warn=True)
xpr.tads = dico['experiments'][name]['tads']
xpr.norm = dico['experiments'][name]['wght']
xpr.hic_data = dico['experiments'][name]['hi-c']
xpr.conditions = dico['experiments'][name]['cond']
xpr.size = dico['experiments'][name]['size']
xpr._zeros = dico['experiments'][name].get('zero', {})
try: # new in version post-CSDM13
xpr.identifier = dico['experiments'][name]['iden']
xpr.cell_type = dico['experiments'][name]['cell']
xpr.exp_type = dico['experiments'][name]['expt']
xpr.enzyme = dico['experiments'][name]['enzy']
xpr.description = dico['experiments'][name]['desc']
except KeyError:
xpr.identifier = None
xpr.cell_type = None
xpr.exp_type = None
xpr.enzyme = None
xpr.description = {}
try:
crm.experiments.append(xpr)
except TypeError:
continue
crm.size = dico['size']
crm.r_size = dico['r_size']
crm.max_tad_size = dico['max_tad_size']
crm.forbidden = dico['forbidden']
crm._centromere = dico['_centromere']
try: # new in version post-CSDM13
crm.species = dico['species']
crm.assembly = dico['assembly']
crm.description = dico['description']
except KeyError:
crm.species = None
crm.assembly = None
crm.description = {}
if isinstance(dico['experiments'][name]['hi-c'], basestring) or fast != int(2):
try:
dicp = load(open(in_f + '_hic','rb'))
for name in dico['experiments']:
crm.get_experiment(name).hic_data = dicp[name]['hi-c']
if fast != 1:
crm.get_experiment(name).norm = dicp[name]['wght']
except IOError:
try:
for name in dico['experiments']:
crm.get_experiment(name).hic_data = dico['experiments'][name]['hi-c']
if fast != 1:
crm.get_experiment(name).norm = dico['experiments'][name]['wght']
except KeyError:
raise Exception('ERROR: file %s not found\n' % (
dico['experiments'][name]['hi-c']))
elif not fast:
stderr.write('WARNING: data not saved correctly for fast loading.\n')
return crm