Commit e29a1702 authored by Ivan Vanát's avatar Ivan Vanát
Browse files

catching exceptions; updated generator argument description

parent 6a1bfadb

nested/cli/generator.py

+3 −3
Original line number Original line Diff line number Diff line
@@ -11,13 +11,13 @@ from nested.output.sketcher import Sketcher 
@click.argument('input_db', required=True, type=click.Path(exists=True))

@click.argument('input_db', required=True, type=click.Path(exists=True))

@click.argument('output_db', required=True, type=str)

@click.argument('output_db', required=True, type=str)

@click.option('--baselength', '-l', type=int, help='Baselength for generated elements.')

@click.option('--baselength', '-l', type=int, help='Baselength for generated elements.')

@click.option('--number_of_iterations', '-i', type=int, help='Number of iterations in generating.')

@click.option('--number_of_iterations', '-i', type=int, help='Number of inserted elements.')

@click.option('--number_of_elements', '-n', type=int, help='Number of generated elements.')

@click.option('--number_of_elements', '-n', type=int, help='Number of generated sequences.')

@click.option('--filter', '-f', is_flag=True, default=False, type=str, help='Filter database and create new one with given output db path.')

@click.option('--filter', '-f', is_flag=True, default=False, type=str, help='Filter database and create new one with given output db path.')

@click.option('--filter_string', '-s', type=str, help='Filter entries by given string [ONLY RELEVANT WITH -filter OPTION].')

@click.option('--filter_string', '-s', type=str, help='Filter entries by given string [ONLY RELEVANT WITH -filter OPTION].')

@click.option('--filter_offset', '-o', type=int, help='LTR offset allowed [ONLY RELEVANT WITH -filter OPTION].')

@click.option('--filter_offset', '-o', type=int, help='LTR offset allowed [ONLY RELEVANT WITH -filter OPTION].')

@click.option('--percentage', '-p', type=int, help='Percentage of elements in generated sequence.')

@click.option('--percentage', '-p', type=int, help='Percentage of elements in generated sequence.')

@click.option('--average_element', '-a', type=int, help='Average element length.')

@click.option('--average_element', '-a', type=int, help='Average element length in database.')

@click.option('--expected_length', '-e', type=int, help='Expected output sequence length [ONLY WORKS WITH -percentage and -average_element].')

@click.option('--expected_length', '-e', type=int, help='Expected output sequence length [ONLY WORKS WITH -percentage and -average_element].')

@click.option('--output_directory', '-d', default=os.getcwd(), type=str, help='Output directory.')

@click.option('--output_directory', '-d', default=os.getcwd(), type=str, help='Output directory.')

def main(input_db, output_db, baselength, number_of_iterations,

def main(input_db, output_db, baselength, number_of_iterations,

nested/cli/nester.py

+21 −21
Original line number Original line Diff line number Diff line
@@ -42,7 +42,7 @@ def process_sequence(sequence, sketcher, i, sketch, format, output_fasta_offset, 
    seq_start_time = datetime.now()

    seq_start_time = datetime.now()

    strlen = 15

    strlen = 15

    print("Processing {}".format(sequence.id))

    print("Processing {}".format(sequence.id))

    #try:

    try:

        nester = Nester(sequence, i, initial_threshold, threshold_multiplier)

        nester = Nester(sequence, i, initial_threshold, threshold_multiplier)

        sketcher.create_gff(nester.nested_element, dirpath=output_folder, output_fasta_offset=output_fasta_offset, format=format)

        sketcher.create_gff(nester.nested_element, dirpath=output_folder, output_fasta_offset=output_fasta_offset, format=format)

        sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)  

        sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)
@@ -52,17 +52,17 @@ def process_sequence(sequence, sketcher, i, sketch, format, output_fasta_offset, 
            sketcher.sketch(sequence.id, dirpath=output_folder)

            sketcher.sketch(sequence.id, dirpath=output_folder)

        seq_end_time = datetime.now()

        seq_end_time = datetime.now()

        print('Processing {a}: DONE [{b}]'.format(a=sequence.id, b=seq_end_time - seq_start_time))

        print('Processing {a}: DONE [{b}]'.format(a=sequence.id, b=seq_end_time - seq_start_time))

    #except KeyboardInterrupt:

    except KeyboardInterrupt:

    #    cleanup()

        cleanup()

    #    raise

        raise

    #except CalledProcessError:

    except CalledProcessError:

    #    cleanup()

        cleanup()

    #    number_of_errors += 1

        number_of_errors += 1

    #    print('Processing {}: SUBPROCESS ERROR'.format(sequence.id[:strlen]))

        print('Processing {}: SUBPROCESS ERROR'.format(sequence.id[:strlen]))

    #except:

    except:

    #    cleanup()

        cleanup()

    #    number_of_errors += 1

        number_of_errors += 1

    #    print('Processing {}: UNEXPECTED ERROR:'.format(sequence.id[:strlen]), sys.exc_info()[0])

        print('Processing {}: UNEXPECTED ERROR:'.format(sequence.id[:strlen]), sys.exc_info()[0])





def cleanup():

def cleanup():

    for file in glob.glob("*ltrs.fa"):

    for file in glob.glob("*ltrs.fa"):