swamp.mr.mr module¶

class Mr(id, target_fa, target_mtz, workdir, phased_mtz=None, logger=None, silent=False)[source]¶

This is an abstract class for MR pipelines. It implements data structures and methods commonly used in MR tasks.

Parameters:

Parameters:	id (str) – unique identifier for the `Mr` instance target_fa (str) – target’s fasta filename target_mtz (str) – target’s mtz filename workdir (str) – working directory where the MR pipeline will be executed phased_mtz (str) – filename of the target’s mtz containing phase information (default None) logger (SwampLogger) – logging interface for the MR pipeline (default None) silent (bool) – if set to True the logger will not print messages (default False)
Variables:	results (list) – A list with the figures of merit obtained after the completion of the pipeline error (bool) – True if errors have occurred at some point on the pipeline results – contains the results obtained in the MR pipeline

id (str) – unique identifier for the Mr instance
target_fa (str) – target’s fasta filename
target_mtz (str) – target’s mtz filename
workdir (str) – working directory where the MR pipeline will be executed
phased_mtz (str) – filename of the target’s mtz containing phase information (default None)
logger (SwampLogger) – logging interface for the MR pipeline (default None)
silent (bool) – if set to True the logger will not print messages (default False)

Variables:

results (list) – A list with the figures of merit obtained after the completion of the pipeline
error (bool) – True if errors have occurred at some point on the pipeline
results – contains the results obtained in the MR pipeline

append_results()[source]¶: Abstract method to append the results obtained so far into results

cleanup_dir_list¶: Abstract property to hold the location of the directories to cleanup after completion of the pipeline

create_result_table_outfile(fname=None)[source]¶

Method to write string representation of table_contents into result_table_fname or into a specific file if fname is set.

Parameters:	fname (str) – filename where the result table will be created (default None)

init_params¶: A dictionary to store the initial parameters used to instantiate the Mr

make_workdir()[source]¶: Method to create the working directory of the Mr instance

result_table_fname¶: Filename where the string representation of table_contents will be written

store_pickle(fname=None, mode='ab')[source]¶

Method to pickle the Mr instance into a file

Parameters:	fname (str) – filename where the pickle will be created (default None) mode (str) – mode that will be used to open the file handle (default ‘ab’)