Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
Batch_manager

Packages

 Batch_manager
 This package provides tools to automate the execution of a given program on a collection of datasets, while varying parameters. Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus
 

Classes

class  BM_Dataset_association_rules
 
class  BM_Run_specification_tuple
 
class  BM_Run_specification_ensemble
 
class  BM_NFO_set
 
class  BM_IFO_set
 
class  BM_Batch
 
class  BM_Dataset
 
class  BM_Database
 

Variables

 file_names
 
 directory
 
 datasets
 
 association_mode_list
 
 arity
 
 executable_path
 
 nvp_list
 
 options_list
 
 general_regex
 
 options_list
 
 option_names
 
 dataset
 
 output_directory
 
 executable_path
 
 NFO
 
 IFO
 
 is_built
 
 output_directory_prefix
 

Built-in Methods

def __init__ (self)
 Initialize an empty dataset. More...
 
def __len__ (self)
 Return the number of files recorded in the dataset. More...
 

Manipulating Data

def get_directory (self)
 Return the directory absolute path. More...
 
def load_from_directory (self, directory, file_name_re=".*", recursive=False)
 Add all file names in an input directory matching the input regular expression (default is all) with a possible recursive rule (default is False). More...
 
def remove_data (self, file_name_re=".*")
 Remove all the file names matching the regular expression (default is all). More...
 
def get_data (self, file_name_re=".*")
 Access to the list of stored file names matching the input regular expression (default is all). More...
 
def get_tuple_data (self, common_regex, regexs, general_regex=None)
 get_tuple_data More...
 

Built-in Methods

def __init__ (self)
 Initialize an empty database with possibly a name. More...
 
def __len__ (self)
 Return the number of datasets recorded in the database. More...
 

Manipulating Datasets

def add_dataset (self, dataset)
 Add a dataset to this database. More...
 
def add_datasets_from_directory (self, directory, file_name_re=".*", recursion_level=0)
 Search recursively in a directory all the files matching the input regular expression, and create one dataset per directory maximally at the input recursion_level. More...
 
def get_datasets (self)
 Return all the recorded datasets. More...
 

Built-in Methods

def __init__ (self)
 Initialize an empty association rule. More...
 

Building Files Tuples

def build_input_files_tuples (self, IFO_regexs, general_regex, dataset)
 Return the list of tuples of files in the dataset matching the association rules. More...
 

Built-in Methods

def __init__ (self, executable_path="")
 Initialize a run specification with possibly the executable path. More...
 
def __len__ (self)
 Return the number of options in the specification. More...
 

Executable Path

def get_run_options (self)
 Return the list of nvp options corresponding to this run. More...
 
def get_executable_path (self)
 Get the executable path. More...
 
def set_executable_path (self, executable_path)
 Set the executable file path. More...
 

Options Management

def add_option (self, name, value="")
 Add the option name for an input option with a given value. More...
 
def add_file_option (self, name, value="")
 Add the option name for an input file option with the path to a file. More...
 
def build_run_command (self)
 Create the command line corresponding to the specified run. More...
 
def run (self)
 Starts the specified run. More...
 

Built-in Methods

def __len__ (self)
 Return the number of run specifications. More...
 

Runs

def add_run_specification (self, run_specification)
 Add a run specification to the list. More...
 
def get_lists_of_run_options (self)
 Return the lists of nvp options corresponding to all runs. More...
 
def get_executable_path (self)
 Get the executable path. More...
 
def build_run_commands (self)
 Build all the run commands from the list of specifications, and return them as a list. More...
 
def run (self, output_directory, nb_instances=1)
 Start all the runs in the list. More...
 

Options Management

def add_option_from_nvp_list (self, nvp_list)
 Creates all the possible tuples of options for a run. More...
 
def build_options_list (self)
 Creates all the possible tuples of options for a run. More...
 
def get_options_list (self)
 Return the list of possible combinations of NFO. More...
 

Options Management

def add_option_from_nvp_list (self, nvp_list)
 Add a nvp to the options list. More...
 
def build_options_list (self, dataset, association_rules)
 From the input dataset and association rules, create the tuples of files. More...
 
def get_options_list (self)
 Return the list of possible combinations of IFO. More...
 

Loading

def set_dataset (self, dataset)
 Set the current dataset from an existing dataset. More...
 
def add_run_specification (self, run_specification)
 Add a simple run specification to the batch. More...
 
def load_dataset (self, directory, file_name_re=".*", recursive=False)
 Load the dataset from a directory. More...
 
def check_specification (self)
 Check that the loaded specification is correct. More...
 
def load_run_specification (self, file_name)
 Load the specification of the runs from a specification file. More...
 

Building the Runs

def build_run_commands (self)
 Builds the run specifications of each run of the batch, and return them. More...
 
def split_per_IFO (self)
 Split the batch such that each new batch is invariant w.r.t the IFO. More...
 
def split_per_NFO (self)
 Split the batch such that each new batch is invariant w.r.t the NFO. More...
 
def split_per_selected_NFO_option (self, option_name)
 Split the batch such that the new batch is invariant w.r.t the input NFO name. More...
 
def split_per_selected_IFO_option (self, option_name)
 Split the batch such that the new batch is invariant w.r.t the input IFO name. More...
 
def split_per_selected_option (self, option_name)
 Split the batch such that the new batch is invariant w.r.t the input option. More...
 
def split_per_selected_options (self, option_names)
 Same as previous but do it recursively over a list of option names. More...
 

Accessing the Runs

def get_output_directory (self)
 Simple access to the directory where the runs of the batch are run. More...
 
def set_output_directory_prefix (self, prefix)
 Sets a prefix for the output directory where the runs of the batch are run. More...
 
def set_output_directory (self, output_directory)
 Sets the output directory, where the runs of the batch are run. More...
 
def get_run_commands (self)
 Simple access to the run specification of each run. More...
 

Starting the Runs

def print_batch (self)
 Print all the run commands from the list of specifications. More...
 
def get_lists_of_run_options (self)
 Return a list of run options for each run in the batch. More...
 
def run (self, nb_instances=1)
 Does the runs nb_instances times. More...
 
def repeat (self, nb_instances)
 Synonym of run, but the number of instances has no default value. More...
 
def make_scripts (self)
 Make one file per execution instead of runnning them. More...
 

Description

                       \class SBL::Batch_manager::BM_Dataset_association_rules
                       \brief Associate a rule between files of a dataset.
                  
  @} 
  \nosubgrouping
                       \class SBL::Batch_manager::BM_NFO_set
                       \brief Set of non-file options with multiple values.

                       \details This data structure provides the method get_options_list allowing to return all possible combination of non-file options for a run.
                  
  @} 
  \nosubgrouping
               \class SBL::Batch_manager::BM_IFO_set
               \brief Set of input file options with multiple values.
               \details This data structure provides the method get_options_list allowing to return all possible tuples of input files for a run.
                  
  @} 
  \nosubgrouping