cluster.py

############################################################################################################
# Authors: 
#   Sebastian Stricker, Uni Heidelberg, sebastian.stricker@stud.uni-heidelberg.de
#   Marcio Ferreira,    EMBL-EBI,       marcio@ebi.ac.uk
# Date: 08/2021
# License: GNU GENERAL PUBLIC LICENSE Version 3
###
# Algorithm routine that is exectued when the cluster option is specified. 
# Deviates slightly from the main file to accomodate the structure of bsub lsf dispatching.
###
############################################################################################################
import logging
import pathlib
import sys

import src.io_operations as io_operations
import src.setup as setup

from numpy import isnan as isnan
import pandas as pd

from medaka_bpm import analyse_directory

LOGGER = logging.getLogger(__name__)

################################## STARTUP SETUP ##################################
if __name__ == '__main__':
    try:
        # Parse input arguments
        args = setup.parse_arguments()

        experiment_id, args = setup.process_arguments(args, is_cluster_node=True)

        # Should receive only a single channel/loop/wellID, it's a cluster node with 1 job.
        # Needed as list though
        channels = list(args.channels)
        loops = list(args.loops)

        tmp_dir = args.outdir / 'tmp'

        if args.lsf_index[0] == '\\':
            # this is for fixing a weird behaviour: the lsf_index comes with a "\" as the first character. The "\" is usefull to pass the parameter, but need to be deleted here.
            args.lsf_index = args.lsf_index[1:]

        well_id = 'WE00' + '{:03d}'.format(int(args.lsf_index))
        analysis_id = channels[0] + '-' + loops[0] + '-' + well_id

        # Check if video for well id exists before producting data.
        if not io_operations.well_video_exists(args.indir, channels[0], loops[0], well_id):
            sys.exit()

        setup.config_logger(tmp_dir, (analysis_id + ".log"), args.debug)

        # Run analysisp
        well_nr = int(well_id[-3:])
        results = analyse_directory(args, channels, loops, wells=[well_nr])

        # write bpm in tmp directory
        out_string = ""
        for col in results.columns:
            value = results[col][0]

            if not pd.isnull(value):
                value = str(value)
            else:
                value = 'NA'

            out_string += f"{col}:{value};"

        out_string = out_string[:-1]

        out_file = tmp_dir / f'{analysis_id}.txt'
        with open(out_file, 'w') as output:
            output.write(out_string)

    except Exception as e:
        LOGGER.exception("In analysis dispatched to a cluster node")