shmir package¶
Submodules¶
shmir.async module¶
- shmir.async.get_async_result(task, task_id, timeout=1.0, only_status=False)¶
Gets AsyncResult of task, excepting TimeoutError and handling failures
- Args:
- task: the task from which want extract result from task_id: id of task timeout(float): timeout of task only_status(bool): boolean if function should return only status (default: False)
- Returns:
- Task response
shmir.contextmanagers module¶
- shmir.contextmanagers.blast_path(*args, **kwds)¶
Context manager which changes path for blast executions
- shmir.contextmanagers.generic_path(path)¶
Function which changes current path to given path
- Args:
- path(str): path where interpreter should be
- shmir.contextmanagers.mfold_path(*args, **kwds)¶
Context manager which changes path for mfold tasks
- Args:
- task_id: id of mfold task
shmir.decorators module¶
- shmir.decorators.catch_errors(*errors)¶
Decorator to catch specific errors given
- Args:
- *errors: All error which should be catched
- Returns:
- dict with error status and its message or function result
- shmir.decorators.send_email(file_handler=None)¶
Decorator to send email after task
- Args:
- file_handler: function to handle files
shmir.mfold module¶
shmir.result_handlers module¶
- shmir.result_handlers.zip_file_mfold(path)¶
Function which creates zip_msg to send via email
- Args:
- path: path of zip file
- Returns:
- tuple of zip message
- shmir.result_handlers.zip_files_from_sirna(struct)¶
Function which generates email msg from siRNA
- Args:
- struct: sh-miR struct
- Returns:
- zip message
- shmir.result_handlers.zip_files_from_transcript(struct)¶
Function which generates email msg from transcript
- Args:
- struct: sh-miR struct
- Returns:
- zip message
shmir.settings module¶
- shmir.settings.get_bool(section, option, default=None)¶
Function which gets settings
- Args:
- section(str): section of settings option(str): option of settings
- Returns:
- config(bool) or default value
- shmir.settings.get_config(section, option, default=None)¶
Function which gets settings
- Args:
- section(str): section of settings option(str): option of settings
- Returns:
- config or default value
- shmir.settings.get_db_config(option, default=None)¶
- shmir.settings.get_int(section, option, default=None)¶
Function which gets settings
- Args:
- section(str): section of settings option(str): option of settings
- Returns:
- config(int) or default value
shmir.testing module¶
- class shmir.testing.TestModelBase(methodName='runTest')¶
Bases: unittest.case.TestCase
- get_all(model)¶
- put_to_db(obj)¶
- setUp()¶
- tearDown()¶
- shmir.testing.create_backbone()¶
Function to create default backbone object
shmir.utils module¶
shmir.views module¶
- shmir.views.mfold_task_creator(*args, **kwargs)¶
Handler to create folded structure via mfold for specific sequence.
- Args:
- data: sequence
- Returns:
- Task id of this task
- shmir.views.mfold_task_result(task_id)¶
Handler for getting mfold result from just a task id
- Args:
- task_id: Id of task generated via RESTful API
- Returns:
- Json object of status or sends zipped file
- shmir.views.mfold_task_status(task_id)¶
Mfold status getter
- Args:
- task_id: Id of task generated via RESTful API
- Returns:
- Json object with status of specific id
- shmir.views.scaffolds(*args, **kwargs)¶
Handler to list all possible backbones
- Returns:
- Json object with names of backbones list
- shmir.views.sirna_task_creator(*args, **kwargs)¶
Handler to initialize task which creates sh-miR(s) from siRNA
- Args:
- data: one siRNA strand (active) or two siRNA strands separated by space.
- First strand is active, both are in 5-3 orientation.
- Returns:
- Task id
- shmir.views.sirna_task_result(task_id)¶
Handler to give result of sh-miR(s) created from siRNA
- Args:
- task_id: Id of task generated via RESTful API
- Returns:
- Json object with sh-miRs created from siRNA: [(score, sh-miR, bacbone name, pdf(id to download pdf via mfold)...]
- shmir.views.sirna_task_status(task_id)¶
Handler to check status of task which creates sh-miR from siRNA
- Args:
- task_id: Id of task generated via RESTful API
- Returns:
- Json object with status of given task_id
- shmir.views.transcript_task_creator(*args, **kwargs)¶
Handler to create sh-miR from transcript
- Args:
- transcript_name: name of transcript
- Returns:
- Id of task
- shmir.views.transcript_task_result(task_id)¶
Handler to get results of task which creates sh-miR(s) from transcript
- Args:
- task_id: Id of task generated via RESTful API
- Returns:
- Json object with list of sh-miRs in structure: [sh-miR, score, pdf(id to download pdf via mfold), sequence and backbone name...]
- shmir.views.transcript_task_status(task_id)¶
Handler to check status of task which creates sh-miR from transcript
- Args:
- task_id: Id of task generated via RESTful API
- Returns:
- Json object with status of given task_id