metaquast.py

#!/usr/bin/env python

############################################################################
# Copyright (c) 2022-2024 Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), HZI
# Copyright (c) 2015-2022 Saint Petersburg State University
# Copyright (c) 2011-2015 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################

import sys
import os
import shutil

try:
   from collections import OrderedDict
except ImportError:
   from quast_libs.site_packages.ordered_dict import OrderedDict

from quast_libs import qconfig
qconfig.check_python_version()

from site import addsitedir
addsitedir(os.path.join(qconfig.LIBS_LOCATION, 'site_packages'))
from quast_libs.metautils import Assembly, correct_meta_references, correct_assemblies, \
    get_downloaded_refs_with_alignments, partition_contigs, calculate_ave_read_support
from quast_libs.options_parser import parse_options, remove_from_quast_py_args, prepare_regular_quast_args

from quast_libs import contigs_analyzer, search_references_meta, plotter_data, qutils, run_busco
from quast_libs.qutils import cleanup, check_dirpath, is_python2, run_parallel

from quast_libs.log import get_logger
logger = get_logger(qconfig.LOGGER_META_NAME)
logger.set_up_console_handler()


def _start_quast_main(args, assemblies, reference_fpath=None, output_dirpath=None, num_notifications_tuple=None,
                      labels=None, run_regular_quast=False, is_combined_ref=False, is_parallel_run=False):
    args = args[:]

    args.extend([asm.fpath for asm in assemblies])

    if reference_fpath:
        args.append('-R')
        args.append(reference_fpath)

    if output_dirpath:
        args.append('-o')
        args.append(output_dirpath)

    args.append('--labels')

    def quote(line):
        if ' ' in line:
            line = '"%s"' % line
        return line

    args.append(quote(', '.join([asm.label for asm in assemblies])))

    import quast
    try:
        import importlib
        importlib.reload(quast)
    except (ImportError, AttributeError):
        reload(quast)
    quast.logger.set_up_console_handler(indent_val=1, debug=qconfig.debug)
    if not run_regular_quast:
        reference_name = os.path.basename(qutils.name_from_fpath(reference_fpath)) if reference_fpath else None
        quast.logger.set_up_metaquast(is_parallel_run=is_parallel_run, ref_name=reference_name)
    if is_combined_ref:
        logger.info_to_file('(logging to ' +
                        os.path.join(output_dirpath, qconfig.LOGGER_DEFAULT_NAME + '.log)'))
    return_code = quast.main(args)
    if num_notifications_tuple:
        cur_num_notifications = quast.logger.get_numbers_of_notifications()
        num_notifications_tuple = list(map(sum, zip(num_notifications_tuple, cur_num_notifications)))

    if is_combined_ref:
        labels[:] = [qconfig.assembly_labels_by_fpath[fpath] for fpath in qconfig.assemblies_fpaths]
        assemblies[:] = [Assembly(fpath, qconfig.assembly_labels_by_fpath[fpath]) for fpath in qconfig.assemblies_fpaths]

    return return_code, num_notifications_tuple


def _run_quast_per_ref(quast_py_args, output_dirpath_per_ref, ref_fpath, ref_assemblies, total_num_notifications, is_parallel_run=False):
    ref_name = qutils.name_from_fpath(ref_fpath)
    if not ref_assemblies:
        logger.main_info('\nNo contigs were aligned to the reference ' + ref_name + ', skipping..')
        output_dirpath = os.path.join(output_dirpath_per_ref, ref_name)
        if not os.path.isdir(output_dirpath):
            os.makedirs(output_dirpath)
        json_text = None
        if qconfig.html_report:
            from quast_libs.html_saver import html_saver, json_saver
            html_saver.save_empty_report(output_dirpath, qconfig.min_contig, ref_fpath)
            json_text = json_saver.json_text
        return ref_name, json_text, total_num_notifications
    else:
        output_dirpath = os.path.join(output_dirpath_per_ref, ref_name)
        run_name = 'for the contigs aligned to ' + ref_name
        logger.main_info('\nStarting quast.py ' + run_name +
                         '... (logging to ' + os.path.join(output_dirpath, qconfig.LOGGER_DEFAULT_NAME) + '.log)')

        return_code, total_num_notifications = _start_quast_main(quast_py_args,
                                                                 assemblies=ref_assemblies,
                                                                 reference_fpath=ref_fpath,
                                                                 output_dirpath=output_dirpath,
                                                                 num_notifications_tuple=total_num_notifications,
                                                                 is_parallel_run=is_parallel_run)
        json_text = None
        if qconfig.html_report:
            from quast_libs.html_saver import json_saver
            json_text = json_saver.json_text
        return ref_name, json_text, total_num_notifications


def main(args):
    check_dirpath(qconfig.QUAST_HOME, 'You are trying to run it from ' + str(qconfig.QUAST_HOME) + '.\n' +
                  'Please, put QUAST in a different directory, then try again.\n', exit_code=3)

    if not args:
        qconfig.usage(stream=sys.stderr)
        sys.exit(1)

    metaquast_path = [os.path.realpath(__file__)]
    quast_py_args, contigs_fpaths = parse_options(logger, metaquast_path + args)
    output_dirpath, ref_fpaths, labels = qconfig.output_dirpath, qconfig.reference, qconfig.labels
    html_report = qconfig.html_report
    test_mode = qconfig.test

    # Directories
    output_dirpath, _, _ = qutils.set_up_output_dir(
        output_dirpath, None, not output_dirpath,
        save_json=False)

    corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)

    qconfig.set_max_threads(logger)
    qutils.logger = logger

    ########################################################################

    from quast_libs import reporting
    try:
        import importlib
        importlib.reload(reporting)
    except (ImportError, AttributeError):
        reload(reporting)
    from quast_libs import plotter

    if os.path.isdir(corrected_dirpath):
        shutil.rmtree(corrected_dirpath)
    os.mkdir(corrected_dirpath)

    # PROCESSING REFERENCES
    if ref_fpaths:
        logger.main_info()
        logger.main_info('Reference(s):')

        corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
            correct_meta_references(ref_fpaths, corrected_dirpath)

    # PROCESSING CONTIGS
    logger.main_info()
    logger.main_info('Contigs:')
    qconfig.no_check_meta = True
    assemblies, labels = correct_assemblies(contigs_fpaths, output_dirpath, labels)
    if not assemblies:
        logger.error("None of the assembly files contains correct contigs. "
                     "Please, provide different files or decrease --min-contig threshold.")
        return 4

    # Running QUAST(s)
    if qconfig.gene_finding:
        quast_py_args += ['--mgm']
    if qconfig.min_IDY is None: # special case: user not specified min-IDY, so we need to use MetaQUAST default value
        quast_py_args += ['--min-identity', str(qconfig.META_MIN_IDY)]

    if qconfig.reuse_combined_alignments:
        reuse_combined_alignments = True
    else:
        reuse_combined_alignments = False

    downloaded_refs = False

    # SEARCHING REFERENCES
    if not ref_fpaths:
        logger.main_info()
        if qconfig.max_references == 0:
            logger.notice("Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled")
        else:
            if qconfig.references_txt:
                logger.main_info("List of references was provided, starting to download reference genomes from NCBI...")
            else:
                logger.main_info("No references are provided, starting to search for reference genomes in SILVA 16S rRNA database "
                        "and to download them from NCBI...")
            downloaded_dirpath = os.path.join(output_dirpath, qconfig.downloaded_dirname)
            if not os.path.isdir(downloaded_dirpath):
                os.mkdir(downloaded_dirpath)
            corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
            ref_fpaths = search_references_meta.do(assemblies, labels, downloaded_dirpath, corrected_dirpath, qconfig.references_txt)
            if ref_fpaths:
                search_references_meta.is_quast_first_run = True
                if not qconfig.references_txt:
                    downloaded_refs = True
                logger.main_info()
                logger.main_info('Downloaded reference(s):')
                corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
                    correct_meta_references(ref_fpaths, corrected_dirpath, downloaded_refs=True)
            elif test_mode and not ref_fpaths:
                logger.error('Failed to download or setup SILVA 16S rRNA database for working without '
                             'references on metagenome datasets!', to_stderr=True, exit_with_code=4)

    if not ref_fpaths:
        # No references, running regular quast with MetaGenemark gene finder
        logger.main_info()
        logger.notice('No references are provided, starting regular QUAST with MetaGeneMark gene finder')
        assemblies = [Assembly(fpath, qutils.label_from_fpath(fpath)) for fpath in contigs_fpaths]
        _start_quast_main(quast_py_args, assemblies=assemblies, output_dirpath=output_dirpath, run_regular_quast=True)
        exit(0)

    # Running combined reference
    combined_output_dirpath = os.path.join(output_dirpath, qconfig.combined_output_name)
    qconfig.reference = combined_ref_fpath

    if qconfig.bed:
        quast_py_args += ['--sv-bed']
        quast_py_args += [qconfig.bed]

    quast_py_args += ['--combined-ref']
    if qconfig.draw_plots or qconfig.html_report:
        if plotter_data.dict_color_and_ls:
            colors_and_ls = [plotter_data.dict_color_and_ls[asm.label] for asm in assemblies]
            quast_py_args += ['--colors']
            quast_py_args += [','.join([style[0] for style in colors_and_ls])]
            quast_py_args += ['--ls']
            quast_py_args += [','.join([style[1] for style in colors_and_ls])]
    run_name = 'for the combined reference'
    logger.main_info()
    logger.main_info('Starting quast.py ' + run_name + '...')
    total_num_notices = 0
    total_num_warnings = 0
    total_num_nf_errors = 0
    total_num_notifications = (total_num_notices, total_num_warnings, total_num_nf_errors)
    if qconfig.html_report:
        from quast_libs.html_saver import json_saver
        json_texts = []
    else:
        json_texts = None
    if qconfig.unique_mapping:
        ambiguity_opts = []
    else:
        ambiguity_opts = ["--ambiguity-usage", 'all']
    return_code, total_num_notifications = \
        _start_quast_main(quast_py_args + ambiguity_opts,
        labels=labels,
        assemblies=assemblies,
        reference_fpath=combined_ref_fpath,
        output_dirpath=combined_output_dirpath,
        num_notifications_tuple=total_num_notifications,
        is_combined_ref=True)

    if json_texts is not None:
        json_texts.append(json_saver.json_text)
    search_references_meta.is_quast_first_run = False

    genome_info_dirpath = os.path.join(output_dirpath, qconfig.combined_output_name, 'genome_stats')
    genome_info_fpath = os.path.join(genome_info_dirpath, 'genome_info.txt')
    if not os.path.exists(genome_info_fpath):
        logger.main_info('')
        if not downloaded_refs:
            msg = 'Try to restart MetaQUAST with another references.'
        else:
            msg = 'Try to use option --max-ref-number to change maximum number of references (per each assembly) to download.'
        logger.main_info('Failed aligning the contigs for all the references. ' + msg)
        logger.main_info('')
        cleanup(corrected_dirpath)
        logger.main_info('MetaQUAST finished.')
        return logger.finish_up(numbers=tuple(total_num_notifications), check_test=test_mode)

    if downloaded_refs and return_code == 0:
        logger.main_info()
        logger.main_info('Excluding downloaded references with low genome fraction from further analysis..')
        corr_ref_fpaths = get_downloaded_refs_with_alignments(genome_info_fpath, ref_fpaths, chromosomes_by_refs)
        if corr_ref_fpaths and corr_ref_fpaths != ref_fpaths:
            logger.main_info()
            logger.main_info('Filtered reference(s):')
            os.remove(combined_ref_fpath)
            contigs_analyzer.ref_labels_by_chromosomes = OrderedDict()
            corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names = \
                correct_meta_references(corr_ref_fpaths, corrected_dirpath)
            assemblies, labels = correct_assemblies(contigs_fpaths, output_dirpath, labels)
            run_name = 'for the corrected combined reference'
            logger.main_info()
            logger.main_info('Starting quast.py ' + run_name + '...')
            return_code, total_num_notifications = \
                _start_quast_main(quast_py_args + ambiguity_opts,
                labels=labels,
                assemblies=assemblies,
                reference_fpath=combined_ref_fpath,
                output_dirpath=combined_output_dirpath,
                num_notifications_tuple=total_num_notifications,
                is_combined_ref=True)
            if json_texts is not None:
                json_texts = json_texts[:-1]
                json_texts.append(json_saver.json_text)
        elif corr_ref_fpaths == ref_fpaths:
            logger.main_info('All downloaded references have genome fraction more than 10%. Nothing was excluded.')
        else:
            logger.main_info('All downloaded references have low genome fraction. Nothing was excluded for now.')

    if return_code != 0:
        logger.main_info('MetaQUAST finished.')
        return logger.finish_up(numbers=tuple(total_num_notifications), check_test=test_mode)

    if qconfig.calculate_read_support:
        calculate_ave_read_support(combined_output_dirpath, assemblies)

    prepare_regular_quast_args(quast_py_args, combined_output_dirpath, reuse_combined_alignments)
    logger.main_info()
    logger.main_info('Partitioning contigs into bins aligned to each reference..')

    assemblies_by_reference, not_aligned_assemblies = partition_contigs(
        assemblies, corrected_ref_fpaths, corrected_dirpath,
        os.path.join(combined_output_dirpath, qconfig.detailed_contigs_reports_dirname, 'alignments_%s.tsv'), labels)

    if qconfig.run_busco:
        db_dirpath = run_busco.download_db(logger, qconfig.prokaryote, is_fungus=qconfig.is_fungus)
        if not db_dirpath:
            remove_from_quast_py_args(quast_py_args, '--conservative')

    output_dirpath_per_ref = os.path.join(output_dirpath, qconfig.per_ref_dirname)
    if not qconfig.memory_efficient and \
                    len(assemblies_by_reference) > len(assemblies) and len(assemblies) < qconfig.max_threads:
        logger.main_info()
        logger.main_info('Run QUAST on different references in parallel..')
        threads_per_ref = max(1, qconfig.max_threads // len(assemblies_by_reference))
        quast_py_args += ['--memory-efficient']
        quast_py_args += ['-t', str(threads_per_ref)]

        num_notifications = (0, 0, 0)
        parallel_run_args = [(quast_py_args, output_dirpath_per_ref, ref_fpath, ref_assemblies, num_notifications, True)
                             for ref_fpath, ref_assemblies in assemblies_by_reference]
        ref_names, ref_json_texts, ref_notifications = \
            run_parallel(_run_quast_per_ref, parallel_run_args, qconfig.max_threads, filter_results=True)
        per_ref_num_notifications = list(map(sum, zip(*ref_notifications)))
        total_num_notifications = list(map(sum, zip(total_num_notifications, per_ref_num_notifications)))
        if json_texts is not None:
            json_texts.extend(ref_json_texts)
        quast_py_args.remove('--memory-efficient')
        quast_py_args = remove_from_quast_py_args(quast_py_args, '-t', str(threads_per_ref))
    else:
        ref_names = []
        for ref_fpath, ref_assemblies in assemblies_by_reference:
            ref_name, json_text, total_num_notifications = \
                _run_quast_per_ref(quast_py_args, output_dirpath_per_ref, ref_fpath, ref_assemblies, total_num_notifications)
            if not ref_name:
                continue
            ref_names.append(ref_name)
            if json_texts is not None:
                json_texts.append(json_text)

    # Finally running for the contigs that has not been aligned to any reference
    no_unaligned_contigs = True
    for assembly in not_aligned_assemblies:
        if os.path.isfile(assembly.fpath) and os.stat(assembly.fpath).st_size != 0:
            no_unaligned_contigs = False
            break

    run_name = 'for the contigs not aligned anywhere'
    logger.main_info()
    if no_unaligned_contigs:
        logger.main_info('Skipping quast.py ' + run_name + ' (everything is aligned!)')
    else:
        logger.main_info('Starting quast.py ' + run_name + '... (logging to ' +
                        os.path.join(output_dirpath, qconfig.not_aligned_name, qconfig.LOGGER_DEFAULT_NAME + '.log)'))

        return_code, total_num_notifications = _start_quast_main(quast_py_args + ['-t', str(qconfig.max_threads)],
            assemblies=not_aligned_assemblies,
            output_dirpath=os.path.join(output_dirpath, qconfig.not_aligned_name),
            num_notifications_tuple=total_num_notifications)

        if return_code not in [0, 4]:
            logger.error('Error running quast.py for the contigs not aligned anywhere')
        elif return_code == 4:  # no unaligned contigs, i.e. everything aligned
            no_unaligned_contigs = True
        if not no_unaligned_contigs:
            if json_texts is not None:
                json_texts.append(json_saver.json_text)

    if ref_names:
        logger.print_timestamp()
        logger.main_info("Summarizing results...")

        summary_output_dirpath = os.path.join(output_dirpath, qconfig.meta_summary_dir)
        if not os.path.isdir(summary_output_dirpath):
            os.makedirs(summary_output_dirpath)
        if html_report and json_texts:
            from quast_libs.html_saver import html_saver
            html_summary_report_fpath = html_saver.init_meta_report(output_dirpath)
        else:
            html_summary_report_fpath = None
        from quast_libs import create_meta_summary
        metrics_for_plots = reporting.Fields.main_metrics
        misassembly_metrics = [reporting.Fields.MIS_RELOCATION, reporting.Fields.MIS_TRANSLOCATION, reporting.Fields.MIS_INVERTION,
                              reporting.Fields.MIS_ISTRANSLOCATIONS]
        if no_unaligned_contigs:
            full_ref_names = [qutils.name_from_fpath(ref_fpath) for ref_fpath in corrected_ref_fpaths]
        else:
            full_ref_names = [qutils.name_from_fpath(ref_fpath) for ref_fpath in corrected_ref_fpaths] + [qconfig.not_aligned_name]
        create_meta_summary.do(html_summary_report_fpath, summary_output_dirpath, combined_output_dirpath,
                               output_dirpath_per_ref, metrics_for_plots, misassembly_metrics, full_ref_names)
        if html_report and json_texts:
            html_saver.save_colors(output_dirpath, contigs_fpaths, plotter_data.dict_color_and_ls, meta=True)
            if qconfig.create_icarus_html:
                icarus_html_fpath = html_saver.create_meta_icarus(output_dirpath, ref_names)
                logger.main_info('  Icarus (contig browser) is saved to %s' % icarus_html_fpath)
            html_saver.create_meta_report(output_dirpath, json_texts)

    cleanup(corrected_dirpath)
    logger.main_info('')
    logger.main_info('MetaQUAST finished.')
    return logger.finish_up(numbers=tuple(total_num_notifications), check_test=test_mode)


if __name__ == '__main__':
    try:
        return_code = main(sys.argv[1:])
        exit(return_code)
    except Exception:
        _, exc_value, _ = sys.exc_info()
        logger.exception(exc_value)
        logger.error('exception caught!', exit_with_code=1, to_stderr=True)