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import abc
from abc import abstractmethod
from ont_fast5_api.fast5_file import Fast5File, Fast5FileTypeError
from ont_fast5_api.fast5_read import Fast5Read
class BaseTool(object):
@property
def group_id(self):
raise NotImplementedError("BaseTool does not have a group_id")
@property
def analysis_id(self):
raise NotImplementedError("BaseTool does not have a analysis_id")
def __init__(self, source, mode='r', group_name=None, meta=None, config=None):
""" Create a new analysis_tools object.
:param source: Either an open Fast5File object, or a filename
of a fast5 file.
:param mode: The open mode (r or r+). Only if a filename is used
for the source argument.
:param group_name: The specific analysis instance you are interested in.
:param meta: Metadata for a new analysis.
:param config: Configuration data for a new analysis.
To create a new analysis group, provide a group name that
does not already exist, and an optional dictionary with the metadata.
The following fields are recommended, as a minimum:
* name - The name of the software used.
* time_stamp - The time at which the analysis was performed.
If the group name already exists, the "meta" parameter is ignored. If
the specified group has a "component" attribute, and its value does not
match self.analysis_id, an exception will be thrown.
"""
if isinstance(source, Fast5Read):
self.filename = source.filename # Useful for debugging purposes
self.handle = source
self.close_handle_when_done = False
elif isinstance(source, str):
self.filename = source # Useful for debugging purposes
try:
self.handle = Fast5File(source, mode)
except Fast5FileTypeError :
raise NotImplementedError("AnalysisTools do not support accessing MultiReadFast5 files by filepath")
self.close_handle_when_done = True
else:
raise KeyError('Unrecognized type for argument "source": {}'.format(source))
if group_name is None:
group_name = self.handle.get_latest_analysis(self.group_id)
if group_name is None:
raise KeyError('No group: {} found in file: {}'.format(group_name, self.filename))
self.group_name = group_name
attrs = self.handle.get_analysis_attributes(group_name)
if attrs is None:
self.handle.add_analysis(self.analysis_id, group_name, meta, config)
attrs = self.handle.get_analysis_attributes(group_name)
if 'component' in attrs and attrs['component'] != self.analysis_id:
raise ValueError('Component {} is not {}'.format(attrs.get('component'), self.analysis_id))
def __enter__(self):
return self
def __exit__(self, exception_type, exception_value, traceback):
self.close()
return False
def close(self):
""" Closes the object.
"""
if self.handle and self.close_handle_when_done:
self.handle.close()
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