run_clans_cmd.py

# The main script for running clans via the command-line (no graphics) #
########################################################################
import time
import os
import clans.config as cfg
import clans.clans.io.parser as parser
import clans.clans.io.file_handler as fh
import clans.clans.similarity_search.blast as blast
import clans.clans.layouts.layout_handler as lh

# Parse the command-line arguments
parser.parse_arguments()
cfg.run_params['working_dir'] = os.getcwd()

# Read the input file (fasta/clans/delimited) and fill the relevant main data-structures
try:
    print("Reading the input file")
    before = time.time()
    fh.read_input_file(cfg.run_params['input_file'], cfg.run_params['input_format'])
    after = time.time()
    duration = (after - before)
    if cfg.run_params['is_problem']:
        print(cfg.run_params['error'])
        exit()
    else:
        if cfg.run_params['is_debug_mode']:
            print("Reading the input file took "+str(duration)+" seconds")

except Exception as err:
    print("An error has occurred while reading the input file")
    print(err)
    exit()

# Perform BLAST search and fill the HSP's E-values in the similarity matrix
try:
    if cfg.run_params['run_blast']:
        print("Running blast")
        before = time.time()
        blast.find_HSPs()
        after = time.time()
        duration = (after - before)
        if cfg.run_params['is_problem']:
            print(cfg.run_params['error'])
            exit()
        else:
            if cfg.run_params['is_debug_mode']:
                print("Performing the BLAST search took " + str(duration) + " seconds")

except Exception as err:
    print("An error has occurred while running the BLAST search")
    print(err)
    exit()

# Run the Fruchterman-Reingold layout calculation for the defined number of rounds
try:
    if cfg.run_params['num_of_rounds'] > 0:
        print("Running clustering of " + str(cfg.run_params['num_of_rounds']) + " rounds")
        before = time.time()
        lh.calculate_layout("FR")
        after = time.time()
        duration = (after - before)
        if cfg.run_params['is_debug_mode'] and cfg.run_params['rounds_done'] % 100 != 0:
            print("The calculation of " + str(cfg.run_params['rounds_done']) + " rounds took " + str(duration) +
                  " seconds")

except Exception as err:
    print("An error has occurred while running the Fruchterman-Reingold layout calculation")
    print(err)
    exit()

## Write the output file
try:
    if cfg.run_params['output_file'] is not None:
        before = time.time()
        fh.write_file(cfg.run_params['output_file'], cfg.run_params['output_format'], 0)
        print("File " + cfg.run_params['output_file'] + " was successfully saved")
        after = time.time()
        duration = (after - before)
        if cfg.run_params['is_debug_mode']:
            print("Writing the output file took "+str(duration)+" seconds")

except Exception as err:
    print("An error has occurred while saving the output file")
    print(err)
    exit()