コード例 #1
0
def parse_options(logger, quast_args):
    mode = get_mode(quast_args[0])
    is_metaquast = True if mode == 'meta' else False
    qconfig.large_genome = True if mode == 'large' else False

    if '-h' in quast_args or '--help' in quast_args or '--help-hidden' in quast_args:
        qconfig.usage('--help-hidden' in quast_args, mode=mode, short=False)
        sys.exit(0)

    if '-v' in quast_args or '--version' in quast_args:
        qconfig.print_version(mode)
        sys.exit(0)

    quast_py_args = quast_args[1:]

    options = [
        (['--debug'], dict(
             dest='debug',
             action='store_true')
         ),
        (['--no-portable-html'], dict(
             dest='portable_html',
             action='store_false')
         ),
        (['--test'], dict(
             dest='test',
             action='store_true')
         ),
        (['--test-sv'], dict(
             dest='test_sv',
             action='store_true')
         ),
        (['--test-no-ref'], dict(
             dest='test_no_ref',
             action='store_true')
         ),
        (['-o', '--output-dir'], dict(
             dest='output_dirpath',
             type='string',
             action='callback',
             callback=check_output_dir,
             callback_args=(logger,))
         ),
        (['-t', '--threads'], dict(
             dest='max_threads',
             type='int',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'default_value': 1, 'min_value': 1})
         ),
        (['-r', '-R', '--reference'], dict(
             dest='reference',
             type='string' if is_metaquast else 'file',
             action='callback' if is_metaquast else 'store',
             callback_args=(logger,) if is_metaquast else None,
             callback=parse_meta_references if is_metaquast else None)
         ),
        (['-O', '--operons'], dict(
             dest='operons',
             type='file',
             action='extend')
         ),
        (['-G', '--genes'], dict(
             dest='genes',
             type='string',
             action='callback',
             callback_args=(logger, True),
             callback=parse_features)
         ),
        (['-g', '--features'], dict(
             dest='features',
             type='string',
             action='callback',
             callback_args=(logger,),
             callback=parse_features)
         ),
        (['-1', '--reads1'], dict(
             dest='forward_reads',
             type='file',
             action='extend')
         ),
        (['-2', '--reads2'], dict(
             dest='reverse_reads',
             type='file',
             action='extend')
         ),
        (['--pe1'], dict(
             dest='forward_reads',
             type='file',
             action='extend')
         ),
        (['--pe2'], dict(
             dest='reverse_reads',
             type='file',
             action='extend')
         ),
        (['--mp1'], dict(
             dest='mp_forward_reads',
             type='file',
             action='extend')
         ),
        (['--mp2'], dict(
             dest='mp_reverse_reads',
             type='file',
             action='extend')
         ),
        (['--12'], dict(
             dest='interlaced_reads',
             type='file',
             action='extend')
         ),
        (['--pe12'], dict(
             dest='interlaced_reads',
             type='file',
             action='extend')
         ),
        (['--mp12'], dict(
             dest='mp_interlaced_reads',
             type='file',
             action='extend')
         ),
        (['--single'], dict(
             dest='unpaired_reads',
             type='file',
             action='extend')
         ),
        (['--pacbio'], dict(
             dest='pacbio_reads',
             type='file',
             action='extend')
         ),
        (['--nanopore'], dict(
             dest='nanopore_reads',
             type='file',
             action='extend')
         ),
        (['--ref-sam'], dict(
            dest='reference_sam',
            type='file')
         ),
        (['--ref-bam'], dict(
            dest='reference_bam',
            type='file')
         ),
        (['--sam'], dict(
            dest='sam_fpaths',
            type='string',
            action='callback',
            callback_args=('.sam', logger),
            callback=parse_files_list)
         ),
        (['--bam'], dict(
            dest='bam_fpaths',
            type='string',
            action='callback',
            callback_args=('.bam', logger),
            callback=parse_files_list)
         ),
        (['--sv-bedpe'], dict(
             dest='bed',
             type='file')
         ),
        (['--cov'], dict(
             dest='cov_fpath',
             type='file')
         ),
        (['--phys-cov'], dict(
             dest='phys_cov_fpath',
             type='file')
         ),
        (['-l', '--labels'], dict(
             dest='labels',
             type='string')
         ),
        (['-L'], dict(
             dest='all_labels_from_dirs',
             action='store_true')
         ),
        (['--mgm'], dict(
             dest='metagenemark',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['gene_finding', 'metagenemark']},
             default=False)
         ),
        (['-s', '--split-scaffolds'], dict(
             dest='split_scaffolds',
             action='store_true')
         ),
        (['-e', '--eukaryote'], dict(
             dest='prokaryote',
             action='store_false')
         ),
        (['--fungus'], dict(
             dest='is_fungus',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['is_fungus'],
                              'store_false_values': ['prokaryote']})
         ),
        (['--large'], dict(
             dest='large_genome',
             action='store_true')
         ),
        (['-f', '--gene-finding'], dict(
             dest='gene_finding',
             action='store_true')
         ),
        (['--rna-finding'], dict(
             dest='rna_gene_finding',
             action='store_true')
         ),
        (['--fragmented'], dict(
             dest='check_for_fragmented_ref',
             action='store_true')
         ),
        (['--fragmented-max-indent'], dict(
             dest='fragmented_max_indent',
             type='int',
             default=qconfig.MAX_INDEL_LENGTH,
             action='callback',
             callback=set_fragmented_max_indent,
             callback_args=(logger,))
         ),
        (['-a', '--ambiguity-usage'], dict(
             dest='ambiguity_usage',
             type='string',
             default=qconfig.ambiguity_usage,
             action='callback',
             callback=check_str_arg_value,
             callback_args=(logger,),
             callback_kwargs={'available_values': ['none', 'one', 'all']})
         ),
        (['--ambiguity-score'], dict(
             dest='ambiguity_score',
             type='float',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 0.8, 'max_value': 1.0})
         ),
        (['-u', '--use-all-alignments'], dict(
             dest='use_all_alignments',
             action='store_true')
         ),
        (['--strict-NA'], dict(
             dest='strict_NA',
             action='store_true')
         ),
        (['--unaligned-part-size'], dict(
             dest='unaligned_part_size',
             type=int)
         ),
        (['--skip-unaligned-mis-contigs'], dict(
            dest='unaligned_mis_threshold',
            action="store_const",
            const=0.0)
         ),
        (['-x', '--extensive-mis-size'], dict(
             dest='extensive_misassembly_threshold',
             type='int',
             default=qconfig.extensive_misassembly_threshold,
             action='callback',
             callback=set_extensive_mis_size,
             callback_args=(logger,))
         ),
        (['--scaffold-gap-max-size'], dict(
             dest='scaffolds_gap_threshold',
             type=int)
         ),
        (['-m', '--min-contig'], dict(
             dest='min_contig',
             type='int')
         ),
        (['-i', '--min-alignment'], dict(
             dest='min_alignment',
             type='int')
         ),
        (['--min-identity'], dict(
             dest='min_IDY',
             type='float',
             default=qconfig.min_IDY,
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 80.0, 'max_value': 100.0})
         ),
        (['--est-ref-size'], dict(
             dest='estimated_reference_size',
             type='int')
         ),
        (['--contig-thresholds'], dict(
             dest='contig_thresholds')
         ),
        (['--gene-thresholds'], dict(
             dest='genes_lengths')
         ),
        (['--glimmer'], dict(
             dest='glimmer',
             action='store_true',
             default=False)
         ),
        (['-b', '--conserved-genes-finding'], dict(
             dest='run_busco',
             action='store_true',
             default=False)
         ),
        (['-k', '--k-mer-stats'], dict(
             dest='use_kmc',
             action='store_true',
             default=False)
         ),
        (['--k-mer-size'], dict(
             dest='unique_kmer_len',
             type='int')
         ),
        (['--upper-bound-assembly'], dict(
             dest='optimal_assembly',
             action='store_true')
         ),
        (['--upper-bound-min-con'], dict(
             dest='upperbound_min_connections',
             type='int',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 1})
         ),
        (['--est-insert-size'], dict(
             dest='optimal_assembly_insert_size',
             type='int',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': qconfig.optimal_assembly_min_IS,
                              'max_value': qconfig.optimal_assembly_max_IS})
         ),
        (['--plots-format'], dict(
             dest='plot_extension',
             type='string',
             action='callback',
             callback=check_str_arg_value,
             callback_args=(logger,),
             callback_kwargs={'available_values': qconfig.supported_plot_extensions})
         ),
        (['--use-input-ref-order'], dict(
             dest='use_input_ref_order',
             action='store_true')
         ),
        (['--circos'], dict(
             dest='draw_circos',
             action='store_true')
         ),
        (['--no-read-stats'], dict(
             dest='no_read_stats',
             action='store_true')
         ),
        (['--fast'], dict(
             dest='fast',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['no_gc', 'no_sv', 'no_gzip', 'no_read_stats'],
                              'store_false_values': ['show_snps', 'draw_plots', 'html_report', 'create_icarus_html', 'analyze_gaps']},
             default=False)
         ),
        (['--no-gzip'], dict(
             dest='no_gzip',
             action='store_true')
         ),
        (['--no-check'], dict(
             dest='no_check',
             action='store_true')
         ),
        (['--no-check-meta'], dict(
             dest='no_check_meta',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['no_check', 'no_check_meta']})
         ),
        (['--no-snps'], dict(
             dest='show_snps',
             action='store_false')
         ),
        (['--no-plots'], dict(
             dest='draw_plots',
             action='store_false')
         ),
        (['--no-html'], dict(
             dest='html_report',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_false_values': ['html_report', 'create_icarus_html']})
         ),
        (['--no-icarus'], dict(
             dest='create_icarus_html',
             action='store_false')
         ),
        (['--no-gc'], dict(
             dest='no_gc',
             action='store_true')
         ),
        (['--no-sv'], dict(
             dest='no_sv',
             action='store_true')
         ),
        (['--memory-efficient'], dict(
             dest='memory_efficient',
             action='store_true')
         ),
        (['--space-efficient'], dict(
             dest='space_efficient',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['space_efficient'],
                              'store_false_values': ['show_snps', 'create_icarus_html']},)
         ),
        (['--silent'], dict(
             dest='silent',
             action='store_true')
         ),
        (['--combined-ref'], dict(
             dest='is_combined_ref',
             action='store_true')
         ),
        (['--colors'], dict(
             dest='used_colors',
             action='extend')
         ),
        (['--ls'], dict(
             dest='used_ls',
             action='extend')
         ),
        (['-j', '--save-json'], dict(
             dest='save_json',
             action='store_true')
         ),
        (['-J', '--save-json-to'], dict(
             dest='json_output_dirpath')
         ),
        (['--err-fpath'], dict(
             dest='error_log_fpath')
         ),
        (['--read-support'], dict(
             dest='calculate_read_support',
             action='store_true')
         )
    ]
    if is_metaquast:
        options += [
            (['--unique-mapping'], dict(
                 dest='unique_mapping',
                 action='store_true')
             ),
            (['--max-ref-number'], dict(
                 dest='max_references',
                 type='int',
                 action='callback',
                 callback=check_arg_value,
                 callback_args=(logger,),
                 callback_kwargs={'default_value': qconfig.max_references, 'min_value': 0})
             ),
            (['--references-list'], dict(
                 dest='references_txt')
             ),
            (['--blast-db'], dict(
                 dest='custom_blast_db_fpath')
             )
        ]

    parser = OptionParser(option_class=QuastOption)
    for args, kwargs in options:
        parser.add_option(*args, **kwargs)
    (opts, contigs_fpaths) = parser.parse_args(quast_args[1:])

    if qconfig.test_sv and is_metaquast:
        msg = "Option --test-sv can be used for QUAST only\n"
        wrong_test_option(logger, msg)
    if qconfig.test_no_ref and not is_metaquast:
        msg = "Option --test-no-ref can be used for MetaQUAST only\n"
        wrong_test_option(logger, msg)

    if qconfig.glimmer and qconfig.gene_finding:
        logger.error("You cannot use --glimmer and " + ("--mgm" if qconfig.metagenemark else "--gene-finding") + \
                     " simultaneously!", exit_with_code=3)

    if qconfig.test or qconfig.test_no_ref or qconfig.test_sv:
        qconfig.output_dirpath = abspath(qconfig.test_output_dirname)
        check_dirpath(qconfig.output_dirpath, 'You are trying to run QUAST from ' + str(os.path.dirname(qconfig.output_dirpath)) + '.\n' +
                      'Please, rerun QUAST from a different directory.')
        if qconfig.test or qconfig.test_sv:
            qconfig.reference = meta_test_references if is_metaquast else test_reference
            if not is_metaquast:
                qconfig.features = test_features
                qconfig.operons = test_operons
                qconfig.glimmer = True
                if not qconfig.large_genome:  # special case -- large mode imposes eukaryote gene finding (GeneMark-ES) and our test data is too small for it.
                    qconfig.gene_finding = True
        if qconfig.test_sv:
            qconfig.forward_reads = test_forward_reads
            qconfig.reverse_reads = test_reverse_reads
        contigs_fpaths += meta_test_contigs_fpaths if is_metaquast else test_contigs_fpaths
        qconfig.test = True

        if any(not isfile(fpath) for fpath in contigs_fpaths):
            logger.info(
                '\nYou are probably running QUAST installed via pip, which does not include test data.\n'
                'This is fine, just start using QUAST on your own data!\n\n'
                'If you still want to run tests, please download and unpack test data to CWD:\n'
                '  wget quast.sf.net/test_data.tar.gz && tar xzf test_data.tar.gz\n')
            sys.exit(2)

    if not contigs_fpaths:
        logger.error("You should specify at least one file with contigs!\n", to_stderr=True)
        qconfig.usage(stream=sys.stderr)
        sys.exit(2)

    if qconfig.large_genome:
        set_large_genome_parameters()

    if qconfig.extensive_misassembly_threshold is None:
        qconfig.extensive_misassembly_threshold = \
            qconfig.LARGE_EXTENSIVE_MIS_THRESHOLD if qconfig.large_genome else qconfig.DEFAULT_EXT_MIS_SIZE
    if qconfig.min_contig is None:
        qconfig.min_contig = qconfig.LARGE_MIN_CONTIG if qconfig.large_genome else qconfig.DEFAULT_MIN_CONTIG
    if qconfig.min_alignment is None:
        qconfig.min_alignment = qconfig.LARGE_MIN_ALIGNMENT if qconfig.large_genome else qconfig.DEFAULT_MIN_ALIGNMENT

    for c_fpath in contigs_fpaths:
        assert_file_exists(c_fpath, 'contigs')

    if qconfig.json_output_dirpath:
        qconfig.save_json = True

    if not qconfig.output_dirpath:
        check_dirpath(os.getcwd(), 'An output path was not specified manually. You are trying to run QUAST from ' + str(os.getcwd()) + '.\n' +
                      'Please, specify a different directory using -o option.')
    qconfig.output_dirpath, qconfig.json_output_dirpath, existing_quast_dir = \
        set_up_output_dir(qconfig.output_dirpath, qconfig.json_output_dirpath, not qconfig.output_dirpath,
                          qconfig.save_json if not is_metaquast else None)

    logger.set_up_file_handler(qconfig.output_dirpath, qconfig.error_log_fpath)
    logger.set_up_console_handler(debug=qconfig.debug)
    logger.print_command_line(quast_args, wrap_after=None, is_main=True)
    logger.start()

    if existing_quast_dir:
        logger.notice("Output directory already exists and looks like a QUAST output dir. "
                      "Existing results can be reused (e.g. previously generated alignments)!")
        qutils.remove_reports(qconfig.output_dirpath)

    if qconfig.labels:
        qconfig.labels = qutils.parse_labels(qconfig.labels, contigs_fpaths)
    qconfig.labels = qutils.process_labels(contigs_fpaths, qconfig.labels, qconfig.all_labels_from_dirs)

    if qconfig.contig_thresholds == "None":
        qconfig.contig_thresholds = []
    else:
        qconfig.contig_thresholds = [int(x) for x in qconfig.contig_thresholds.split(",")]
    if qconfig.genes_lengths == "None":
        qconfig.genes_lengths = []
    else:
        qconfig.genes_lengths = [int(x) for x in qconfig.genes_lengths.split(",")]

    qconfig.set_max_threads(logger)

    if parser.values.ambiguity_score:
        if qconfig.ambiguity_usage != 'all':
            qconfig.ambiguity_usage = 'all'
            logger.notice("--ambiguity-usage was set to 'all' because not default --ambiguity-score was specified")

    if is_metaquast:
        quast_py_args = clean_metaquast_args(quast_py_args, contigs_fpaths)

    if qconfig.sam_fpaths or qconfig.bam_fpaths:
        check_sam_bam_files(contigs_fpaths, qconfig.sam_fpaths, qconfig.bam_fpaths, logger)

    return quast_py_args, contigs_fpaths
コード例 #2
0
ファイル: options_parser.py プロジェクト: student-t/quast
def parse_options(logger, quast_args, is_metaquast=False):
    if '-h' in quast_args or '--help' in quast_args or '--help-hidden' in quast_args:
        qconfig.usage('--help-hidden' in quast_args, meta=is_metaquast, short=False)
        sys.exit(0)

    if '-v' in quast_args or '--version' in quast_args:
        qconfig.print_version(meta=is_metaquast)
        sys.exit(0)

    quast_py_args = quast_args[1:]

    options = [
        (['--debug'], dict(
             dest='debug',
             action='store_true')
         ),
        (['--no-portable-html'], dict(
             dest='portable_html',
             action='store_false')
         ),
        (['--test'], dict(
             dest='test',
             action='store_true')
         ),
        (['--test-sv'], dict(
             dest='test_sv',
             action='store_true')
         ),
        (['--test-no-ref'], dict(
             dest='test_no_ref',
             action='store_true')
         ),
        (['-o', '--output-dir'], dict(
             dest='output_dirpath',
             type='string',
             action='callback',
             callback=check_output_dir,
             callback_args=(logger,))
         ),
        (['-t', '--threads'], dict(
             dest='max_threads',
             type='int',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'default_value': 1, 'min_value': 1})
         ),
        (['-R', '--reference'], dict(
             dest='reference',
             type='string' if is_metaquast else 'file',
             action='callback' if is_metaquast else 'store',
             callback_args=(logger,) if is_metaquast else None,
             callback=parse_meta_references if is_metaquast else None)
         ),
        (['-G', '--genes'], dict(
             dest='genes',
             type='file',
             action='extend')
         ),
        (['-O', '--operons'], dict(
             dest='operons',
             type='file',
             action='extend')
         ),
        (['-1', '--reads1'], dict(
             dest='forward_reads',
             type='file',
             action='extend')
         ),
        (['-2', '--reads2'], dict(
             dest='reverse_reads',
             type='file',
             action='extend')
         ),
        (['--pe1'], dict(
             dest='forward_reads',
             type='file',
             action='extend')
         ),
        (['--pe2'], dict(
             dest='reverse_reads',
             type='file',
             action='extend')
         ),
        (['--mp1'], dict(
             dest='mp_forward_reads',
             type='file',
             action='extend')
         ),
        (['--mp2'], dict(
             dest='mp_reverse_reads',
             type='file',
             action='extend')
         ),
        (['--12'], dict(
             dest='interlaced_reads',
             type='file',
             action='extend')
         ),
        (['--pe12'], dict(
             dest='interlaced_reads',
             type='file',
             action='extend')
         ),
        (['--mp12'], dict(
             dest='mp_interlaced_reads',
             type='file',
             action='extend')
         ),
        (['--single'], dict(
             dest='unpaired_reads',
             type='file',
             action='extend')
         ),
        (['--ref-sam'], dict(
            dest='reference_sam',
            type='file')
         ),
        (['--ref-bam'], dict(
            dest='reference_bam',
            type='file')
         ),
        (['--sam'], dict(
            dest='sam_fpaths',
            type='string',
            action='callback',
            callback_args=('.sam', logger),
            callback=parse_files_list)
         ),
        (['--bam'], dict(
            dest='bam_fpaths',
            type='string',
            action='callback',
            callback_args=('.bam', logger),
            callback=parse_files_list)
         ),
        (['--sv-bedpe'], dict(
             dest='bed',
             type='file')
         ),
        (['--cov'], dict(
             dest='cov_fpath',
             type='file')
         ),
        (['--phys-cov'], dict(
             dest='phys_cov_fpath',
             type='file')
         ),
        (['-l', '--labels'], dict(
             dest='labels',
             type='string')
         ),
        (['-L'], dict(
             dest='all_labels_from_dirs',
             action='store_true')
         ),
        (['--mgm'], dict(
             dest='metagenemark',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['gene_finding', 'metagenemark']},
             default=False)
         ),
        (['-s', '--scaffolds'], dict(
             dest='scaffolds',
             action='store_true')
         ),
        (['-e', '--eukaryote'], dict(
             dest='prokaryote',
             action='store_false')
         ),
        (['--fungus'], dict(
             dest='is_fungus',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['is_fungus'],
                              'store_false_values': ['prokaryote']})
         ),
        (['--large'], dict(
             dest='large_genome',
             action='store_true')
         ),
        (['-f', '--gene-finding'], dict(
             dest='gene_finding',
             action='store_true')
         ),
        (['--rna-finding'], dict(
             dest='rna_gene_finding',
             action='store_true')
         ),
        (['--fragmented'], dict(
             dest='check_for_fragmented_ref',
             action='store_true')
         ),
        (['--fragmented-max-indent'], dict(
             dest='fragmented_max_indent',
             type='int',
             default=qconfig.MAX_INDEL_LENGTH,
             action='callback',
             callback=set_fragmented_max_indent,
             callback_args=(logger,))
         ),
        (['-a', '--ambiguity-usage'], dict(
             dest='ambiguity_usage',
             type='string',
             default=qconfig.ambiguity_usage,
             action='callback',
             callback=check_str_arg_value,
             callback_args=(logger,),
             callback_kwargs={'available_values': ['none', 'one', 'all']})
         ),
        (['--ambiguity-score'], dict(
             dest='ambiguity_score',
             type='float',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 0.8, 'max_value': 1.0})
         ),
        (['-u', '--use-all-alignments'], dict(
             dest='use_all_alignments',
             action='store_true')
         ),
        (['--strict-NA'], dict(
             dest='strict_NA',
             action='store_true')
         ),
        (['--unaligned-part-size'], dict(
             dest='unaligned_part_size',
             type=int)
         ),
        (['-x', '--extensive-mis-size'], dict(
             dest='extensive_misassembly_threshold',
             type='int',
             default=qconfig.extensive_misassembly_threshold,
             action='callback',
             callback=set_extensive_mis_size,
             callback_args=(logger,))
         ),
        (['--scaffold-gap-max-size'], dict(
             dest='scaffolds_gap_threshold',
             type=int)
         ),
        (['-m', '--min-contig'], dict(
             dest='min_contig',
             type='int')
         ),
        (['-c', '--min-cluster'], dict(
             dest='min_cluster',
             type='int')
         ),
        (['-i', '--min-alignment'], dict(
             dest='min_alignment',
             type='int')
         ),
        (['--min-identity'], dict(
             dest='min_IDY',
             type='float',
             default=qconfig.min_IDY,
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 80.0, 'max_value': 100.0})
         ),
        (['--est-ref-size'], dict(
             dest='estimated_reference_size',
             type='int')
         ),
        (['--contig-thresholds'], dict(
             dest='contig_thresholds')
         ),
        (['--gene-thresholds'], dict(
             dest='genes_lengths')
         ),
        (['--glimmer'], dict(
             dest='glimmer',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['gene_finding', 'glimmer']},
             default=False)
         ),
        (['-b', '--find-conserved-genes'], dict(
             dest='run_busco',
             action='store_true',
             default=False)
         ),
        (['--ideal_assembly'], dict(
             dest='ideal_assembly',
             action='store_true')
         ),
        (['--est-insert-size'], dict(
             dest='ideal_assembly_insert_size',
             type='int',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': qconfig.ideal_assembly_min_IS,
                              'max_value': qconfig.ideal_assembly_max_IS})
         ),
        (['--plots-format'], dict(
             dest='plot_extension',
             type='string',
             action='callback',
             callback=check_str_arg_value,
             callback_args=(logger,),
             callback_kwargs={'available_values': qconfig.supported_plot_extensions})
         ),
        (['--use-input-ref-order'], dict(
             dest='use_input_ref_order',
             action='store_true')
         ),
        (['--svg'], dict(
             dest='draw_svg',
             action='store_true')
         ),
        (['--fast'], dict(
             dest='fast',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['no_gc', 'no_sv', 'no_gzip'],
                              'store_false_values': ['show_snps', 'draw_plots', 'html_report', 'create_icarus_html']},
             default=False)
         ),
        (['--no-gzip'], dict(
             dest='no_gzip',
             action='store_true')
         ),
        (['--no-check'], dict(
             dest='no_check',
             action='store_true')
         ),
        (['--no-check-meta'], dict(
             dest='no_check_meta',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['no_check', 'no_check_meta']})
         ),
        (['--no-snps'], dict(
             dest='show_snps',
             action='store_false')
         ),
        (['--no-plots'], dict(
             dest='draw_plots',
             action='store_false')
         ),
        (['--no-html'], dict(
             dest='html_report',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_false_values': ['html_report', 'create_icarus_html']})
         ),
        (['--no-icarus'], dict(
             dest='create_icarus_html',
             action='store_false')
         ),
        (['--no-gc'], dict(
             dest='no_gc',
             action='store_true')
         ),
        (['--no-sv'], dict(
             dest='no_sv',
             action='store_true')
         ),
        (['--memory-efficient'], dict(
             dest='memory_efficient',
             action='store_true')
         ),
        (['--space-efficient'], dict(
             dest='space_efficient',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['space_efficient'],
                              'store_false_values': ['create_icarus_html']},)
         ),
        (['--force-nucmer'], dict(
             dest='force_nucmer',
             action='store_true')
         ),
        (['--silent'], dict(
             dest='silent',
             action='store_true')
         ),
        (['--combined-ref'], dict(
             dest='is_combined_ref',
             action='store_true')
         ),
        (['--colors'], dict(
             dest='used_colors',
             action='extend')
         ),
        (['--ls'], dict(
             dest='used_ls',
             action='extend')
         ),
        (['-j', '--save-json'], dict(
             dest='save_json',
             action='store_true')
         ),
        (['-J', '--save-json-to'], dict(
             dest='json_output_dirpath')
         ),
        (['--err-fpath'], dict(
             dest='error_log_fpath')
         ),
        (['--read-support'], dict(
             dest='calculate_read_support',
             action='store_true')
         )
    ]
    if is_metaquast:
        options += [
            (['--unique-mapping'], dict(
                 dest='unique_mapping',
                 action='store_true')
             ),
            (['--max-ref-number'], dict(
                 dest='max_references',
                 type='int',
                 action='callback',
                 callback=check_arg_value,
                 callback_args=(logger,),
                 callback_kwargs={'default_value': qconfig.max_references, 'min_value': 0})
             ),
            (['--references-list'], dict(
                 dest='references_txt')
             ),
            (['--blast-db'], dict(
                 dest='custom_blast_db_fpath')
             )
        ]

    parser = OptionParser(option_class=QuastOption)
    for args, kwargs in options:
        parser.add_option(*args, **kwargs)
    (opts, contigs_fpaths) = parser.parse_args(quast_args[1:])

    if qconfig.test_sv and is_metaquast:
        msg = "Option --test-sv can be used for QUAST only\n"
        wrong_test_option(logger, msg, is_metaquast)
    if qconfig.test_no_ref and not is_metaquast:
        msg = "Option --test-no-ref can be used for MetaQUAST only\n"
        wrong_test_option(logger, msg, is_metaquast)

    if qconfig.test or qconfig.test_no_ref or qconfig.test_sv:
        qconfig.output_dirpath = abspath(qconfig.test_output_dirname)
        check_dirpath(qconfig.output_dirpath, 'You are trying to run QUAST from ' + str(os.path.dirname(qconfig.output_dirpath)) + '.\n' +
                  'Please, rerun QUAST from a different directory.')
        if qconfig.test or qconfig.test_sv:
            qconfig.reference = meta_test_references if is_metaquast else test_reference
            if not is_metaquast:
                qconfig.genes = test_genes
                qconfig.operons = test_operons
                qconfig.glimmer = True
                qconfig.gene_finding = True
        if qconfig.test_sv:
            qconfig.forward_reads = test_forward_reads
            qconfig.reverse_reads = test_reverse_reads
        contigs_fpaths += meta_test_contigs_fpaths if is_metaquast else test_contigs_fpaths
        qconfig.test = True
        
        if any(not isfile(fpath) for fpath in contigs_fpaths):
            logger.info(
                '\nYou are probably running QUAST installed via pip, which does not include test data.\n'
                'This is fine, just start using QUAST on your own data!\n'
                'If you still want to run tests, please download test_data directory from \n'
                'https://github.com/ablab/quast/ to CWD, or install QUAST from source:\n'
                'git clone https://github.com/ablab/quast && cd quast && ./setup.py install\n')
            sys.exit(2)

    if not contigs_fpaths:
        logger.error("You should specify at least one file with contigs!\n", to_stderr=True)
        qconfig.usage(meta=is_metaquast, stream=sys.stderr)
        sys.exit(2)

    if qconfig.large_genome:
        set_large_genome_parameters()

    for c_fpath in contigs_fpaths:
        assert_file_exists(c_fpath, 'contigs')

    if qconfig.json_output_dirpath:
        qconfig.save_json = True

    if not qconfig.output_dirpath:
        check_dirpath(os.getcwd(), 'An output path was not specified manually. You are trying to run QUAST from ' + str(os.getcwd()) + '.\n' +
                  'Please, specify a different directory using -o option.')
    qconfig.output_dirpath, qconfig.json_output_dirpath, existing_alignments = \
        set_up_output_dir(qconfig.output_dirpath, qconfig.json_output_dirpath, not qconfig.output_dirpath,
                          qconfig.save_json if not is_metaquast else None)

    logger.set_up_file_handler(qconfig.output_dirpath, qconfig.error_log_fpath)
    logger.set_up_console_handler(debug=qconfig.debug)
    logger.print_command_line(quast_args, wrap_after=None, is_main=True)
    logger.start()

    if existing_alignments and not is_metaquast:
        logger.notice("Output directory already exists. Existing Nucmer alignments can be used")
        qutils.remove_reports(qconfig.output_dirpath)

    if qconfig.labels:
        qconfig.labels = qutils.parse_labels(qconfig.labels, contigs_fpaths)
    qconfig.labels = qutils.process_labels(contigs_fpaths, qconfig.labels, qconfig.all_labels_from_dirs)

    if qconfig.contig_thresholds == "None":
        qconfig.contig_thresholds = []
    else:
        qconfig.contig_thresholds = [int(x) for x in qconfig.contig_thresholds.split(",")]
    if qconfig.genes_lengths == "None":
        qconfig.genes_lengths = []
    else:
        qconfig.genes_lengths = [int(x) for x in qconfig.genes_lengths.split(",")]

    qconfig.set_max_threads(logger)

    if parser.values.ambiguity_score:
        if qconfig.ambiguity_usage != 'all':
            qconfig.ambiguity_usage = 'all'
            logger.notice("--ambiguity-usage was set to 'all' because not default --ambiguity-score was specified")

    if is_metaquast:
        quast_py_args = clean_metaquast_args(quast_py_args, contigs_fpaths)

    if qconfig.sam_fpaths or qconfig.bam_fpaths:
        check_sam_bam_files(contigs_fpaths, qconfig.sam_fpaths, qconfig.bam_fpaths, logger)

    return quast_py_args, contigs_fpaths
コード例 #3
0
def parse_options(logger, quast_args, is_metaquast=False):
    if '-h' in quast_args or '--help' in quast_args or '--help-hidden' in quast_args:
        qconfig.usage('--help-hidden' in quast_args,
                      meta=is_metaquast,
                      short=False)
        sys.exit(0)

    if '-v' in quast_args or '--version' in quast_args:
        qconfig.print_version(meta=is_metaquast)
        sys.exit(0)

    quast_py_args = quast_args[1:]

    options = [
        (['--debug'], dict(dest='debug', action='store_true')),
        (['--no-portable-html'],
         dict(dest='portable_html', action='store_false')),
        (['--test'], dict(dest='test', action='store_true')),
        (['--test-sv'], dict(dest='test_sv', action='store_true')),
        (['--test-no-ref'], dict(dest='test_no_ref', action='store_true')),
        (['-o', '--output-dir'],
         dict(dest='output_dirpath',
              type='string',
              action='callback',
              callback=check_output_dir,
              callback_args=(logger, ))),
        (['-t', '--threads'],
         dict(dest='max_threads',
              type='int',
              action='callback',
              callback=check_arg_value,
              callback_args=(logger, ),
              callback_kwargs={
                  'default_value': 1,
                  'min_value': 1
              })),
        (['-R', '--reference'],
         dict(dest='reference',
              type='string' if is_metaquast else 'file',
              action='callback' if is_metaquast else 'store',
              callback_args=(logger, ) if is_metaquast else None,
              callback=parse_meta_references if is_metaquast else None)),
        (['-G', '--genes'], dict(dest='genes', type='file', action='extend')),
        (['-O', '--operons'], dict(dest='operons',
                                   type='file',
                                   action='extend')),
        (['-1', '--reads1'], dict(dest='forward_reads', type='file')),
        (['-2', '--reads2'], dict(dest='reverse_reads', type='file')),
        (['--sam'], dict(dest='sam', type='file')),
        (['--bam'], dict(dest='bam', type='file')),
        (['--sv-bedpe'], dict(dest='bed', type='file')),
        (['--cov'], dict(dest='cov_fpath', type='file')),
        (['--phys-cov'], dict(dest='phys_cov_fpath', type='file')),
        (['-l', '--labels'], dict(dest='labels', type='string')),
        (['-L'], dict(dest='all_labels_from_dirs', action='store_true')),
        (['--mgm'],
         dict(dest='metagenemark',
              action='callback',
              callback=set_multiple_variables,
              callback_kwargs={
                  'store_true_values': ['gene_finding', 'metagenemark']
              },
              default=False)),
        (['-s', '--scaffolds'], dict(dest='scaffolds', action='store_true')),
        (['-e', '--eukaryote'], dict(dest='prokaryote', action='store_false')),
        (['-f',
          '--gene-finding'], dict(dest='gene_finding', action='store_true')),
        (['--fragmented'],
         dict(dest='check_for_fragmented_ref', action='store_true')),
        (['--fragmented-max-indent'],
         dict(dest='fragmented_max_indent',
              type='int',
              default=qconfig.MAX_INDEL_LENGTH,
              action='callback',
              callback=set_fragmented_max_indent,
              callback_args=(logger, ))),
        (['-a', '--ambiguity-usage'],
         dict(dest='ambiguity_usage',
              type='string',
              default=qconfig.ambiguity_usage,
              action='callback',
              callback=check_str_arg_value,
              callback_args=(logger, ),
              callback_kwargs={'available_values': ['none', 'one', 'all']})),
        (['--ambiguity-score'],
         dict(dest='ambiguity_score',
              type='float',
              action='callback',
              callback=check_arg_value,
              callback_args=(logger, ),
              callback_kwargs={
                  'min_value': 0.8,
                  'max_value': 1.0
              })),
        (['-u', '--use-all-alignments'],
         dict(dest='use_all_alignments', action='store_true')),
        (['--strict-NA'], dict(dest='strict_NA', action='store_true')),
        (['--unaligned-part-size'], dict(dest='unaligned_part_size',
                                         type=int)),
        (['-x', '--extensive-mis-size'],
         dict(dest='extensive_misassembly_threshold',
              type='int',
              default=qconfig.extensive_misassembly_threshold,
              action='callback',
              callback=set_extensive_mis_size,
              callback_args=(logger, ))),
        (['--scaffold-gap-max-size'],
         dict(dest='scaffolds_gap_threshold', type=int)),
        (['-m', '--min-contig'], dict(dest='min_contig', type='int')),
        (['-c', '--min-cluster'], dict(dest='min_cluster', type='int')),
        (['-i', '--min-alignment'], dict(dest='min_alignment', type='int')),
        (['--min-identity'],
         dict(dest='min_IDY',
              type='float',
              default=qconfig.min_IDY,
              action='callback',
              callback=check_arg_value,
              callback_args=(logger, ),
              callback_kwargs={
                  'min_value': 80.0,
                  'max_value': 100.0
              })),
        (['--est-ref-size'], dict(dest='estimated_reference_size',
                                  type='int')),
        (['--contig-thresholds'], dict(dest='contig_thresholds')),
        (['--gene-thresholds'], dict(dest='genes_lengths')),
        (['--gage'], dict(dest='with_gage', action='store_true')),
        (['--glimmer'],
         dict(dest='glimmer',
              action='callback',
              callback=set_multiple_variables,
              callback_kwargs={
                  'store_true_values': ['gene_finding', 'glimmer']
              },
              default=False)),
        (['--plots-format'],
         dict(dest='plot_extension',
              type='string',
              action='callback',
              callback=check_str_arg_value,
              callback_args=(logger, ),
              callback_kwargs={
                  'available_values': qconfig.supported_plot_extensions
              })),
        (['--use-input-ref-order'],
         dict(dest='use_input_ref_order', action='store_true')),
        (['--svg'], dict(dest='draw_svg', action='store_true')),
        (['--fast'],
         dict(dest='fast',
              action='callback',
              callback=set_multiple_variables,
              callback_kwargs={
                  'store_true_values': ['no_gc', 'no_sv', 'no_gzip'],
                  'store_false_values': [
                      'show_snps', 'draw_plots', 'html_report',
                      'create_icarus_html'
                  ]
              },
              default=False)),
        (['--no-gzip'], dict(dest='no_gzip', action='store_true')),
        (['--no-check'], dict(dest='no_check', action='store_true')),
        (['--no-check-meta'],
         dict(dest='no_check_meta',
              action='callback',
              callback=set_multiple_variables,
              callback_kwargs={
                  'store_true_values': ['no_check', 'no_check_meta']
              })), (['--no-snps'], dict(dest='show_snps',
                                        action='store_false')),
        (['--no-plots'], dict(dest='draw_plots', action='store_false')),
        (['--no-html'],
         dict(dest='html_report',
              action='callback',
              callback=set_multiple_variables,
              callback_kwargs={
                  'store_false_values': ['html_report', 'create_icarus_html']
              })),
        (['--no-icarus'], dict(dest='create_icarus_html',
                               action='store_false')),
        (['--no-gc'], dict(dest='no_gc', action='store_true')),
        (['--no-sv'], dict(dest='no_sv', action='store_true')),
        (['--memory-efficient'],
         dict(dest='memory_efficient', action='store_true')),
        (['--space-efficient'],
         dict(
             dest='space_efficient',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={
                 'store_true_values': ['space_efficient'],
                 'store_false_values': ['create_icarus_html']
             },
         )),
        (['--force-nucmer'], dict(dest='force_nucmer', action='store_true')),
        (['--silent'], dict(dest='silent', action='store_true')),
        (['--combined-ref'], dict(dest='is_combined_ref',
                                  action='store_true')),
        (['--colors'], dict(dest='used_colors', action='extend')),
        (['--ls'], dict(dest='used_ls', action='extend')),
        (['-j', '--save-json'], dict(dest='save_json', action='store_true')),
        (['-J', '--save-json-to'], dict(dest='json_output_dirpath')),
        (['--err-fpath'], dict(dest='error_log_fpath')),
        (['--read-support'],
         dict(dest='calculate_read_support', action='store_true'))
    ]
    if is_metaquast:
        options += [(['--unique-mapping'],
                     dict(dest='unique_mapping', action='store_true')),
                    (['--max-ref-number'],
                     dict(dest='max_references',
                          type='int',
                          action='callback',
                          callback=check_arg_value,
                          callback_args=(logger, ),
                          callback_kwargs={
                              'default_value': qconfig.max_references,
                              'min_value': 0
                          })),
                    (['--references-list'], dict(dest='references_txt')),
                    (['--blast-db'], dict(dest='custom_blast_db_fpath'))]

    parser = OptionParser(option_class=QuastOption)
    for args, kwargs in options:
        parser.add_option(*args, **kwargs)
    (opts, contigs_fpaths) = parser.parse_args(quast_args[1:])

    if qconfig.test_sv and is_metaquast:
        msg = "Option --test-sv can be used for QUAST only\n"
        wrong_test_option(logger, msg, is_metaquast)
    if qconfig.test_no_ref and not is_metaquast:
        msg = "Option --test-no-ref can be used for MetaQUAST only\n"
        wrong_test_option(logger, msg, is_metaquast)

    if qconfig.test or qconfig.test_no_ref or qconfig.test_sv:
        qconfig.output_dirpath = abspath(qconfig.test_output_dirname)
        check_dirpath(
            qconfig.output_dirpath, 'You are trying to run QUAST from ' +
            str(os.path.dirname(qconfig.output_dirpath)) + '.\n' +
            'Please, rerun QUAST from a different directory.')
        if qconfig.test or qconfig.test_sv:
            qconfig.reference = meta_test_references if is_metaquast else test_reference
            if not is_metaquast:
                qconfig.genes = test_genes
                qconfig.operons = test_operons
                qconfig.glimmer = True
                qconfig.gene_finding = True
        if qconfig.test_sv:
            qconfig.forward_reads = test_forward_reads
            qconfig.reverse_reads = test_reverse_reads
        contigs_fpaths += meta_test_contigs_fpaths if is_metaquast else test_contigs_fpaths
        qconfig.test = True

        if any(not isfile(fpath) for fpath in contigs_fpaths):
            logger.info(
                '\nYou are probably running QUAST installed via pip, which does not include test data.\n'
                'This is fine, just start using QUAST on your own data!\n\n'
                'If you still want to run tests, please download and unpack test data to CWD:\n'
                '  wget quast.sf.net/test_data.tar.gz && tar xzf test_data.tar.gz\n'
            )
            sys.exit(2)

    if not contigs_fpaths:
        logger.error("You should specify at least one file with contigs!\n",
                     to_stderr=True)
        qconfig.usage(meta=is_metaquast, stream=sys.stderr)
        sys.exit(2)

    for c_fpath in contigs_fpaths:
        assert_file_exists(c_fpath, 'contigs')

    if qconfig.json_output_dirpath:
        qconfig.save_json = True

    if not qconfig.output_dirpath:
        check_dirpath(
            os.getcwd(),
            'An output path was not specified manually. You are trying to run QUAST from '
            + str(os.getcwd()) + '.\n' +
            'Please, specify a different directory using -o option.')
    qconfig.output_dirpath, qconfig.json_output_dirpath, existing_alignments = \
        set_up_output_dir(qconfig.output_dirpath, qconfig.json_output_dirpath, not qconfig.output_dirpath,
                          qconfig.save_json if not is_metaquast else None)

    logger.set_up_file_handler(qconfig.output_dirpath, qconfig.error_log_fpath)
    logger.set_up_console_handler(debug=qconfig.debug)
    logger.print_command_line(quast_args, wrap_after=None, is_main=True)
    logger.start()

    if existing_alignments and not is_metaquast:
        logger.notice(
            "Output directory already exists. Existing Nucmer alignments can be used"
        )
        qutils.remove_reports(qconfig.output_dirpath)

    if qconfig.labels:
        qconfig.labels = qutils.parse_labels(qconfig.labels, contigs_fpaths)
    qconfig.labels = qutils.process_labels(contigs_fpaths, qconfig.labels,
                                           qconfig.all_labels_from_dirs)

    if qconfig.contig_thresholds == "None":
        qconfig.contig_thresholds = []
    else:
        qconfig.contig_thresholds = [
            int(x) for x in qconfig.contig_thresholds.split(",")
        ]
    if qconfig.genes_lengths == "None":
        qconfig.genes_lengths = []
    else:
        qconfig.genes_lengths = [
            int(x) for x in qconfig.genes_lengths.split(",")
        ]

    qconfig.set_max_threads(logger)

    if parser.values.ambiguity_score:
        if qconfig.ambiguity_usage != 'all':
            qconfig.ambiguity_usage = 'all'
            logger.notice(
                "--ambiguity-usage was set to 'all' because not default --ambiguity-score was specified"
            )

    if is_metaquast:
        quast_py_args = clean_metaquast_args(quast_py_args, contigs_fpaths)

    return quast_py_args, contigs_fpaths
コード例 #4
0
def parse_options(logger, quast_args, is_metaquast=False):
    if '-h' in quast_args or '--help' in quast_args or '--help-hidden' in quast_args:
        qconfig.usage('--help-hidden' in quast_args, meta=is_metaquast, short=False)
        sys.exit(0)

    if '-v' in quast_args or '--version' in quast_args:
        qconfig.print_version(meta=is_metaquast)
        sys.exit(0)

    quast_py_args = quast_args[1:]

    options = [
        (['--debug'], dict(
             dest='debug',
             action='store_true')
         ),
        (['--test'], dict(
             dest='test',
             action='store_true')
         ),
        (['--test-sv'], dict(
             dest='test_sv',
             action='store_true')
         ),
        (['--test-no-ref'], dict(
             dest='test_no_ref',
             action='store_true')
         ),
        (['-o', '--output-dir'], dict(
             dest='output_dirpath',
             type='string',
             action='callback',
             callback=check_output_dir,
             callback_args=(logger,))
         ),
        (['-t', '--threads'], dict(
             dest='max_threads',
             type='int',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'default_value': 1, 'min_value': 1})
         ),
        (['-R', '--reference'], dict(
             dest='reference',
             type='string' if is_metaquast else 'file',
             action='callback' if is_metaquast else 'store',
             callback_args=(logger,) if is_metaquast else None,
             callback=parse_meta_references if is_metaquast else None)
         ),
        (['-G', '--genes'], dict(
             dest='genes',
             type='file',
             action='extend')
         ),
        (['-O', '--operons'], dict(
             dest='operons',
             type='file',
             action='extend')
         ),
        (['-1', '--reads1'], dict(
             dest='forward_reads',
             type='file')
         ),
        (['-2', '--reads2'], dict(
             dest='reverse_reads',
             type='file')
         ),
        (['--sam'], dict(
             dest='sam',
             type='file')
         ),
        (['--bam'], dict(
             dest='bam',
             type='file')
         ),
        (['--sv-bedpe'], dict(
             dest='bed',
             type='file')
         ),
        (['-l', '--labels'], dict(
             dest='labels',
             type='string')
         ),
        (['-L'], dict(
             dest='all_labels_from_dirs',
             action='store_true')
         ),
        (['--meta'], dict(
             dest='meta',
             action='store_true')
         ),
        (['-s', '--scaffolds'], dict(
             dest='scaffolds',
             action='store_true')
         ),
        (['-e', '--eukaryote'], dict(
             dest='prokaryote',
             action='store_false')
         ),
        (['-f', '--gene-finding'], dict(
             dest='gene_finding',
             action='store_true')
         ),
        (['--fragmented'], dict(
             dest='check_for_fragmented_ref',
             action='store_true')
         ),
        (['-a', '--ambiguity-usage'], dict(
             dest='ambiguity_usage',
             type='string',
             default=qconfig.ambiguity_usage,
             action='callback',
             callback=check_str_arg_value,
             callback_args=(logger,),
             callback_kwargs={'available_values': ['none', 'one', 'all']})
         ),
        (['--ambiguity-score'], dict(
             dest='ambiguity_score',
             type='float',
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 0.8, 'max_value': 1.0})
         ),
        (['-u', '--use-all-alignments'], dict(
             dest='use_all_alignments',
             action='store_true')
         ),
        (['--strict-NA'], dict(
             dest='strict_NA',
             action='store_true')
         ),
        (['--significant-part-size'], dict(
             dest='significant_part_size',
             type=int)
         ),
        (['-x', '--extensive-mis-size'], dict(
             dest='extensive_misassembly_threshold',
             type='int',
             default=qconfig.extensive_misassembly_threshold,
             action='callback',
             callback=set_extensive_mis_size,
             callback_args=(logger,))
         ),
        (['-m', '--min-contig'], dict(
             dest='min_contig',
             type='int')
         ),
        (['-c', '--min-cluster'], dict(
             dest='min_cluster',
             type='int')
         ),
        (['-i', '--min-alignment'], dict(
             dest='min_alignment',
             type='int')
         ),
        (['--min-identity'], dict(
             dest='min_IDY',
             type='float',
             default=qconfig.min_IDY,
             action='callback',
             callback=check_arg_value,
             callback_args=(logger,),
             callback_kwargs={'min_value': 80.0, 'max_value': 100.0})
         ),
        (['--est-ref-size'], dict(
             dest='estimated_reference_size',
             type='int')
         ),
        (['--contig-thresholds'], dict(
             dest='contig_thresholds')
         ),
        (['--gene-thresholds'], dict(
             dest='genes_lengths')
         ),
        (['--gage'], dict(
             dest='with_gage',
             action='store_true')
         ),
        (['--glimmer'], dict(
             dest='glimmer',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['gene_finding', 'glimmer']},
             default=False)
         ),
        (['--plots-format'], dict(
             dest='plot_extension',
             type='string',
             action='callback',
             callback=check_str_arg_value,
             callback_args=(logger,),
             callback_kwargs={'available_values': qconfig.supported_plot_extensions})
         ),
        (['--svg'], dict(
             dest='draw_svg',
             action='store_true')
         ),
        (['--fast'], dict(
             dest='fast',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['no_gc', 'no_sv', 'no_gzip'],
                              'store_false_values': ['show_snps', 'draw_plots', 'html_report', 'create_icarus_html']},
             default=False)
         ),
        (['--no-gzip'], dict(
             dest='no_gzip',
             action='store_true')
         ),
        (['--no-check'], dict(
             dest='no_check',
             action='store_true')
         ),
        (['--no-check-meta'], dict(
             dest='no_check_meta',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_true_values': ['no_check', 'no_check_meta']})
         ),
        (['--no-snps'], dict(
             dest='show_snps',
             action='store_false')
         ),
        (['--no-plots'], dict(
             dest='draw_plots',
             action='store_false')
         ),
        (['--no-html'], dict(
             dest='html_report',
             action='callback',
             callback=set_multiple_variables,
             callback_kwargs={'store_false_values': ['html_report', 'create_icarus_html']})
         ),
        (['--no-icarus'], dict(
             dest='create_icarus_html',
             action='store_false')
         ),
        (['--no-gc'], dict(
             dest='no_gc',
             action='store_true')
         ),
        (['--no-sv'], dict(
             dest='no_sv',
             action='store_true')
         ),
        (['--memory-efficient'], dict(
             dest='memory_efficient',
             action='store_true')
         ),
        (['--silent'], dict(
             dest='silent',
             action='store_true')
         ),
        (['--combined-ref'], dict(
             dest='is_combined_ref',
             action='store_true')
         ),
        (['--colors'], dict(
             dest='used_colors',
             action='extend')
         ),
        (['--ls'], dict(
             dest='used_ls',
             action='extend')
         ),
        (['-j', '--save-json'], dict(
             dest='save_json',
             action='store_true')
         ),
        (['-J', '--save-json-to'], dict(
             dest='json_output_dirpath')
         ),
        (['--err-fpath'], dict(
             dest='error_log_fpath')
         ),
        (['--read-support'], dict(
             dest='calculate_read_support',
             action='store_true')
         )
    ]
    if is_metaquast:
        options += [
            (['--unique-mapping'], dict(
                 dest='unique_mapping',
                 action='store_true')
             ),
            (['--max-ref-number'], dict(
                 dest='max_references',
                 type='int',
                 action='callback',
                 callback=check_arg_value,
                 callback_args=(logger,),
                 callback_kwargs={'default_value': qconfig.max_references, 'min_value': 0})
             ),
            (['--references-list'], dict(
                 dest='references_txt')
             )
        ]

    parser = OptionParser(option_class=QuastOption)
    for args, kwargs in options:
        parser.add_option(*args, **kwargs)
    (opts, contigs_fpaths) = parser.parse_args(quast_args[1:])

    if qconfig.test_sv and is_metaquast:
        msg = "Option --test-sv can be used for QUAST only\n"
        wrong_test_option(logger, msg, is_metaquast)
    if qconfig.test_no_ref and not is_metaquast:
        msg = "Option --test-no-ref can be used for MetaQUAST only\n"
        wrong_test_option(logger, msg, is_metaquast)

    if qconfig.test or qconfig.test_no_ref or qconfig.test_sv:
        qconfig.output_dirpath = abspath(qconfig.test_output_dirname)
        if qconfig.test or qconfig.test_sv:
            qconfig.reference = meta_test_references if is_metaquast else test_reference
            if not is_metaquast:
                qconfig.genes = test_genes
                qconfig.operons = test_operons
                qconfig.with_gage = True
                qconfig.glimmer = True
                qconfig.gene_finding = True
                qconfig.prokaryote = False
        if qconfig.test_sv:
            qconfig.forward_reads = test_forward_reads
            qconfig.reverse_reads = test_reverse_reads
        contigs_fpaths += meta_test_contigs_fpaths if is_metaquast else test_contigs_fpaths
        qconfig.test = True

    if not contigs_fpaths:
        logger.error("You should specify at least one file with contigs!\n")
        qconfig.usage(meta=is_metaquast)
        sys.exit(2)

    logger.set_up_console_handler(debug=qconfig.debug)

    for c_fpath in contigs_fpaths:
        assert_file_exists(c_fpath, 'contigs')

    if qconfig.json_output_dirpath:
        qconfig.save_json = True

    qconfig.output_dirpath, qconfig.json_output_dirpath, existing_alignments = \
        set_up_output_dir(qconfig.output_dirpath, qconfig.json_output_dirpath, not qconfig.output_dirpath,
                          qconfig.save_json if not is_metaquast else None)

    logger.set_up_file_handler(qconfig.output_dirpath, qconfig.error_log_fpath)
    logger.print_command_line(quast_args, wrap_after=None, is_main=True)
    logger.start()

    if existing_alignments and not is_metaquast:
        logger.notice("Output directory already exists. Existing Nucmer alignments can be used")
        qutils.remove_reports(qconfig.output_dirpath)

    if qconfig.labels:
        qconfig.labels = qutils.parse_labels(qconfig.labels, contigs_fpaths)
    qconfig.labels = qutils.process_labels(contigs_fpaths, qconfig.labels, qconfig.all_labels_from_dirs)

    if qconfig.contig_thresholds == "None":
        qconfig.contig_thresholds = []
    else:
        qconfig.contig_thresholds = map(int, qconfig.contig_thresholds.split(","))
    if qconfig.genes_lengths == "None":
        qconfig.genes_lengths = []
    else:
        qconfig.genes_lengths = map(int, qconfig.genes_lengths.split(","))

    qconfig.set_max_threads(logger)

    if parser.values.ambiguity_score:
        if qconfig.ambiguity_usage != 'all':
            qconfig.ambiguity_usage = 'all'
            logger.notice("--ambiguity-usage was set to 'all' because not default --ambiguity-score was specified")

    if is_metaquast:
        quast_py_args = clean_metaquast_args(quast_py_args, contigs_fpaths)

    return quast_py_args, contigs_fpaths