def __call__(self, data_file, read_file, reference_file, output="Resequencing", min_length=500):
# Validate and set-up run-specific values
self._counter = 0
data_file = validate_file(data_file)
read_file = validate_file(read_file)
reference_file = validate_file(reference_file)
self.initialize_output(output)
# Next we run the 5-step Quiver Process
whitelist_file = self.create_whitelist(read_file)
self.create_fai(reference_file)
rgnh5_file = self.create_rgnh5(data_file, whitelist_file)
cmph5_file = self.run_pbalign(data_file, reference_file, rgnh5_file, min_length)
consensus_file = self.run_quiver(cmph5_file, reference_file)
return consensus_file
def validate_program(self, programs):
# First we try to find the program in the local path
program_paths = [which(program) for program in programs]
program_paths = [path for path in program_paths if path is not None]
print programs
print program_paths
if program_paths:
return program_paths[0]
elif self.setup is None:
msg = 'No program from the set "%s" found in PATH and no SMRT Analysis supplied' % str(
programs)
log.error(msg)
raise IOError(msg)
# Fallback to the Setup Script if needed
setup_programs = [
os.path.join(self.setup, 'analysis/bin', p) for p in programs
]
setup_programs = [validate_file(p) for p in setup_programs]
setup_programs = [path for path in setup_programs if path is not None]
if setup_programs:
return setup_programs[0]
else:
msg = 'No program from the set "%s" found in either PATH or SMRT Analysis env' % str(
programs)
log.error(msg)
raise IOError(msg)
def get_barcode_reader( barcode_file ):
barcode_file = validate_file( barcode_file )
if barcode_file.endswith('.fofn'):
log.info("Barcode input is Fofn, initializing BarcodeH5Collection")
return BarcodeH5Fofn( barcode_file )
elif barcode_file.endswith('.bc.h5'):
log.info("Barcode input is BcH5, initializing BarcodeH5Reader")
return BarcodeH5Reader( barcode_file )
else:
raise ValueError
def validate_setup_path(self, setup):
setup = os.path.abspath(setup)
if setup.endswith("/etc/setup.sh"):
setup = setup[:-13]
print setup
setup_script = os.path.join(setup, "etc/setup.sh")
print setup_script
if not validate_file(setup_script):
msg = "Supplied setup-script does not appear to be valid"
log.error(msg)
raise ValueError(msg)
return setup
def __call__(self,
data_file,
read_file,
reference_file,
output='Resequencing',
min_length=500):
# Validate and set-up run-specific values
self._counter = 0
data_file = validate_file(data_file)
read_file = validate_file(read_file)
reference_file = validate_file(reference_file)
self.initialize_output(output)
# Next we run the 5-step Quiver Process
whitelist_file = self.create_whitelist(read_file)
self.create_fai(reference_file)
rgnh5_file = self.create_rgnh5(data_file, whitelist_file)
cmph5_file = self.run_pbalign(data_file, reference_file, rgnh5_file,
min_length)
consensus_file = self.run_quiver(cmph5_file, reference_file)
return consensus_file
def validate_setup_path(self, setup):
setup = os.path.abspath(setup)
if setup.endswith('/etc/setup.sh'):
setup = setup[:-13]
print setup
setup_script = os.path.join(setup, 'etc/setup.sh')
print setup_script
if not validate_file(setup_script):
msg = "Supplied setup-script does not appear to be valid"
log.error(msg)
raise ValueError(msg)
return setup
def get_bash5_reader(bash5_file):
bash5_file = validate_file(bash5_file)
if bash5_file.endswith('.fofn'):
log.info("Raw data input is Fofn, initializing BasH5Collection")
return BasH5Collection(bash5_file)
elif bash5_file.endswith('.bas.h5'):
log.info("Raw data input is BasH5, initializing BasH5Reader")
return BasH5Reader(bash5_file)
elif bash5_file.endswith('.bax.h5'):
log.info("Raw data input is BaxH5, initializing BaxH5Reader")
return BaxH5Reader(bash5_file)
else:
raise ValueError
def get_bash5_reader(bash5_file):
bash5_file = validate_file(bash5_file)
if bash5_file.endswith(".fofn"):
log.info("Raw data input is Fofn, initializing BasH5Collection")
return BasH5Collection(bash5_file)
elif bash5_file.endswith(".bas.h5"):
log.info("Raw data input is BasH5, initializing BasH5Reader")
return BasH5Reader(bash5_file)
elif bash5_file.endswith(".bax.h5"):
log.info("Raw data input is BaxH5, initializing BaxH5Reader")
return BaxH5Reader(bash5_file)
else:
raise ValueError
def get_bash5_reader( bash5_file ):
bash5_file = validate_file( bash5_file )
if bash5_file.endswith('.fofn'):
log.info("Raw data input is Fofn, initializing BasH5Collection")
c = BasH5Collection( bash5_file )
assert len(c.movieNames) == 1 # Currently we only accept single-movies
return c
elif bash5_file.endswith('.bas.h5'):
log.info("Raw data input is BasH5, initializing BasH5Reader")
return BasH5Reader( bash5_file )
elif bash5_file.endswith('.bax.h5'):
log.info("Raw data input is BaxH5, initializing BaxH5Reader")
return BaxH5Reader( bash5_file )
else:
raise ValueError
def get_bash5_reader(bash5_file):
bash5_file = validate_file(bash5_file)
if bash5_file.endswith('.fofn'):
log.info("Raw data input is Fofn, initializing BasH5Collection")
c = BasH5Collection(bash5_file)
assert len(c.movieNames) == 1 # Currently we only accept single-movies
return c
elif bash5_file.endswith('.bas.h5'):
log.info("Raw data input is BasH5, initializing BasH5Reader")
return BasH5Reader(bash5_file)
elif bash5_file.endswith('.bax.h5'):
log.info("Raw data input is BaxH5, initializing BaxH5Reader")
return BaxH5Reader(bash5_file)
else:
raise ValueError
def validate_program(self, programs):
# First we try to find the program in the local path
program_paths = [which(program) for program in programs]
program_paths = [path for path in program_paths if path is not None]
print programs
print program_paths
if program_paths:
return program_paths[0]
elif self.setup is None:
msg = 'No program from the set "%s" found in PATH and no SMRT Analysis supplied' % str(programs)
log.error(msg)
raise IOError(msg)
# Fallback to the Setup Script if needed
setup_programs = [os.path.join(self.setup, "analysis/bin", p) for p in programs]
setup_programs = [validate_file(p) for p in setup_programs]
setup_programs = [path for path in setup_programs if path is not None]
if setup_programs:
return setup_programs[0]
else:
msg = 'No program from the set "%s" found in either PATH or SMRT Analysis env' % str(programs)
log.error(msg)
raise IOError(msg)
def check_output(self):
return validate_file(self.output)
def check_output(self):
return validate_file( self.output )
def check_arguments(self):
assert self.prefix_arg
assert not validate_file(self.output)
def check_arguments(self):
assert self.prefix_arg
assert not validate_file(self.output)
