class SmrtCell(object):
'''
Initializes a new SmrtCell object from a smrtcell xml file
@param xml_file: the path to a subreadset.xml file of a smrtcell
'''
def __init__(self,xml_file):
self.__logger = logging.getLogger('support.smrtcell')
self.__is_valid = False
self.__xml_file = check_file(xml_file)
if not self.__xml_file:
self.show_log('error', 'XML file '+self.__xml_file+' does not exist or is not a file!')
return
#TODO: read xml content from encrypted file
self.__subreadset = None
try:
self.__subreadset = SubreadSet(self.__xml_file)
except IOError as err:
self.show_log('error', 'Parsing of XML file '+self.__xml_file+' was not successful: '+err+'!')
return
self.__is_valid = True
'''
Tests if the SmrtCell object is valid.
@return: return true if the SmrtCell object is valid otherwise false
@rtype: bool
'''
def is_valid(self):
return self.__is_valid
'''
Returns the name of the SmrtCell object.
@return: the name
@rtype: str
'''
def get_name(self):
return self.__subreadset.name if self.__is_valid else None
'''
Returns the total number of reads in the SmrtCell object.
@return: the number of reads
@rtype: integer
'''
def get_total_number_of_reads(self):
return int(self.__subreadset.metadata.numRecords) if self.__is_valid else None
'''
Returns the total number of bp in the SmrtCell object.
@return: the number of bp
@rtype: integer
'''
def get_total_sum_of_bp(self):
return int(self.__subreadset.metadata.totalLength) if self.__is_valid else None
'''
Returns the number of collections ('sequencing runs') in the SmrtCell object.
Should be 1 in almost all cases. If not, all other functions have an optional argument
to specify the collection.
@return: the number of sequencing runs
@rtype: integer
'''
def get_number_of_collections(self):
return len(self.__subreadset.metadata.collections) if self.__is_valid else None
'''
Checks if a provided collection index is valid, i.e. can access a collection.
Do not confuse with collection index.
@param collection_index: the index of the collection
@return: true if collection index is valid otherwise false
@rtype: bool
'''
def check_collection_index(self,collection_index):
return self.__is_valid and collection_index >= 0 and collection_index<len(self.__subreadset.metadata.collections)
'''
Returns the names of the samples that were loaded onto this SmrtCell.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: a list with sample names
@rtype: list of str
'''
def get_biosample_names(self,collection_index=0):
biosample_names = []
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
num_biosamples = len(self.__subreadset.metadata.collections[collection_index].wellSample.bioSamples)
for i in range(0,num_biosamples):
biosample_names.append(self.__subreadset.metadata.collections[collection_index].wellSample.bioSamples[i].name)
return biosample_names
'''
Returns the cell index.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the cell index
@rtype: integer
'''
def get_cell_index(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return int(self.__subreadset.metadata.collections[collection_index].cellIndex)
else:
return None
'''
Returns the collection number.
Do not confuse with collection index.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the collection number
@rtype: integer
'''
def get_collection_number(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return int(self.__subreadset.metadata.collections[collection_index].collectionNumber)
else:
return None
'''
Returns the raw data path.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the raw data path
@rtype: str
'''
def get_raw_data_path(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return get_absolute_path(self.__subreadset.metadata.collections[collection_index].primary.outputOptions.collectionPathUri)
else:
return None
'''
Returns the run id.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the run id
@rtype: str
'''
def get_run_id(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].runDetails.timeStampedName
else:
return None
'''
Returns the run name.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the run name
@rtype: str
'''
def get_run_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].runDetails.name
else:
return None
'''
Returns the cellpac barcode.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the cellpac barcode
@rtype: str
'''
def get_cellpac_barcode(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].cellPac.barcode
else:
return None
'''
Returns the cellpac lot number.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the cellpac lot number
@rtype: str
'''
def get_cellpac_lot_number(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].cellPac.lotNumber
else:
return None
'''
Returns the instrument code.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the instrument code
@rtype: str
'''
def get_instrument_code(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].instrumentName
else:
return None
'''
Returns the sequencing date.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the sequencing date as string
@rtype: str
'''
def get_sequencing_date(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
val = self.__subreadset.metadata.collections[collection_index].createdAt
reduced_date_string, suffix = val.split(".")
suffix = suffix
return datetime.strptime(reduced_date_string, "%Y-%m-%dT%H:%M:%S").strftime('%Y-%m-%d')
else:
return None
'''
Returns the well name.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the well name
@rtype: str
'''
def get_well_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].wellSample.name
else:
return None
'''
Returns the concentration.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the concentration
@rtype: float
'''
def get_concentration(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return float(self.__subreadset.metadata.collections[collection_index].wellSample.concentration)
else:
return None
'''
Returns the UseCount property.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the UseCount property
@rtype: str
'''
def get_usecount(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].wellSample.useCount
else:
return None
'''
Returns the instrument control software version.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the instrument control software version
@rtype: str
'''
def get_instrument_control_software_version(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].instCtrlVer
else:
return None
'''
Returns the signal processing software version.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the signal processing software version
@rtype: str
'''
def get_signal_processing_software_version(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].sigProcVer
else:
return None
'''
Returns the notes (i.e. additional free text description).
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the notes
@rtype: str
'''
def get_notes(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].wellSample.description
else:
return None
'''
Returns the automation parameters.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: a hash with key - value pairs
@rtype: dict of str
'''
def get_automation_parameters(self,collection_index=0):
automation_parameters = {}
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
for i in range(0,len(self.__subreadset.metadata.collections[collection_index].automation.automationParameters)):
hashed_data = self.__subreadset.metadata.collections[collection_index].automation.automationParameters[i].metadata
automation_parameters[hashed_data['Name']] = hashed_data['SimpleValue']
return automation_parameters
'''
Returns the movie length in minutes.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the movie length in minutes
@rtype: integer
'''
def get_movie_length(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
automation_parameters = self.get_automation_parameters(collection_index)
return int(automation_parameters['MovieLength'])
else:
return None
'''
Returns the immobilization time in minutes.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the immobilization time in minutes
@rtype: integer
'''
def get_immobilisation_time(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
automation_parameters = self.get_automation_parameters(collection_index)
return int(automation_parameters['ImmobilizationTime'])
else:
return None
'''
Returns the insert size.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the insert size
@rtype: integer
'''
def get_insert_size(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
automation_parameters = self.get_automation_parameters(collection_index)
return int(automation_parameters['InsertSize'])
else:
return None
'''
Returns true if hot start was enabled otherwise false.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: true if hot start was enabled false otherwise
@rtype: bool
'''
def get_stage_hotstart_enabled(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return bool(self.__subreadset.metadata.collections[collection_index].wellSample.stageHotstartEnabled)
else:
return None
'''
Returns the primary protocol name
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the primary protocol name
@rtype: str
'''
def get_primary_protocol_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].primary.automationName
else:
return None
'''
Returns the primary protocol config
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the primary protocol config
@rtype: str
'''
def get_primary_protocol_config(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].primary.configFileName
else:
return None
'''
Returns the adapter sequences used in template prep
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: a dictionary with left adapter sequence and right adapter sequence
@rtype: dict of str
'''
def get_adapter_sequences(self,collection_index=0):
adapter_sequences = {}
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
adapter_sequences['LeftAdapterSequence'] = self.__subreadset.metadata.collections[collection_index].templatePrepKit.leftAdaptorSequence
adapter_sequences['RightAdapterSequence'] = self.__subreadset.metadata.collections[collection_index].templatePrepKit.rightAdaptorSequence
return adapter_sequences
'''
Returns the sample name. Deprecated, use get_biosample_names instead.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the sample name
@rtype: str
'''
def get_sample_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
return self.__subreadset.metadata.collections[collection_index].wellSample.name
else:
return None
'''
Returns the name of the Sequel binding kit.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the binding kit name
@rtype: str
'''
def get_binding_kit_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
name = self.__subreadset.metadata.collections[collection_index].bindingKit.name
return normalize('NFKD',name).encode('ascii','ignore')
return
else:
return None
'''
Returns the name of the Sequel template prep kit.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the template prep kit name
@rtype: str
'''
def get_template_prep_kit_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
name = self.__subreadset.metadata.collections[collection_index].templatePrepKit.name
return normalize('NFKD',name).encode('ascii','ignore')
return
else:
return None
'''
Returns the name of the Sequel sequencing plate kit.
@param collection_index: the index of the collection (optional, zero-based, default: 0)
@return: the sequencing plate kit name
@rtype: str
'''
def get_sequencing_plate_kit_name(self,collection_index=0):
if self.__is_valid:
assert self.check_collection_index(collection_index),'Specified collection index is invalid!'
name = self.__subreadset.metadata.collections[collection_index].sequencingKitPlate.name
return normalize('NFKD',name).encode('ascii','ignore')
return
else:
return None
'''
Make all paths encoded in the SmrtCell object relative.
@param outdir: a directory from which the paths should originate (optional, default: ".")
'''
def make_paths_relative(self,outdir="."):
if self.__is_valid:
self.__subreadset.makePathsRelative(outdir)
'''
Make all paths encoded in the SmrtCell object absolute.
'''
def make_paths_absolute(self):
if self.__is_valid:
self.__subreadset.makePathsAbsolute()
'''
Write new (subreadset) xml file for SmrtCell object.
@param filename: a file name
'''
def write(self,filename):
if self.__is_valid:
self.__subreadset.write(filename)
'''
Helper function for log messages
@param level: the log level (debug, info, warning, error, critical)
@param message: the log message
'''
def show_log(self, level, message):
if level == 'debug':
self.__logger.debug(message)
elif level == 'info':
self.__logger.info(message)
elif level == 'warning':
self.__logger.warning(message)
elif level == 'error':
self.__logger.error(message)
elif level == 'critical':
self.__logger.critical(message)
