Example #1
0
def print_ds_output(output_dir, log):
    consensus_file = os.path.join(output_dir, "consensus_contigs.fasta")
    if os.path.exists(consensus_file):
        log.info(" * Assembled consensus contigs are in: " + support.process_spaces(consensus_file))

    paired_consensus_file = os.path.join(output_dir, "paired_consensus_contigs.fasta")
    if os.path.exists(paired_consensus_file):
        log.info(" * Assembled paired consensus contigs are in: " + support.process_spaces(paired_consensus_file))

    unpaired_consensus_file = os.path.join(output_dir, "unpaired_consensus_contigs.fasta")
    if os.path.exists(unpaired_consensus_file):
        log.info(" * Assembled unpaired consensus contigs are in: " + support.process_spaces(unpaired_consensus_file))

    hapalignment_file = os.path.join(output_dir, "haplocontigs_alignent")
    if os.path.exists(hapalignment_file):
        log.info(" * Alignment of haplocontigs is in: " + support.process_spaces(hapalignment_file))

    haplotype_assembly_file = os.path.join(output_dir, "haplotype_assembly.out")
    if os.path.exists(haplotype_assembly_file):
        log.info(" * Results of haplotype assembly are in: " + support.process_spaces(haplotype_assembly_file))

    consregions_file = os.path.join(output_dir, "conservative_regions.fasta")
    if os.path.exists(consregions_file):
        log.info(" * Conservative regions are in: " + support.process_spaces(consregions_file))

    possconsregions_file = os.path.join(output_dir, "possibly_conservative_regions.fasta")
    if os.path.exists(possconsregions_file):
        log.info(" * Possibly conservative regions are in: " + support.process_spaces(possconsregions_file))
Example #2
0
def main(args):
    os.environ["LC_ALL"] = "C"

    if len(args) == 1:
        options_storage.usage(spades_version)
        sys.exit(0)

    log = logging.getLogger('spades')
    log.setLevel(logging.DEBUG)

    console = logging.StreamHandler(sys.stdout)
    console.setFormatter(logging.Formatter('%(message)s'))
    console.setLevel(logging.DEBUG)
    log.addHandler(console)

    support.check_binaries(bin_home, log)

    # parse options and safe all parameters to cfg
    cfg, dataset_data = fill_cfg(args, log)

    if options_storage.continue_mode:
        cmd_line, options = get_options_from_params(os.path.join(options_storage.output_dir, "params.txt"))
        if not options:
            support.error("failed to parse command line of the previous run! Please restart from the beginning or specify another output directory.")
        cfg, dataset_data = fill_cfg(options, log)
        if options_storage.restart_from:
            check_cfg_for_restart_from(cfg)
        options_storage.continue_mode = True

    log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
    if options_storage.continue_mode:
        log_handler = logging.FileHandler(log_filename, mode='a')
    else:
        log_handler = logging.FileHandler(log_filename, mode='w')
    log.addHandler(log_handler)

    if options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline continued. Log can be found here: " + log_filename + "\n")
        log.info("Restored from " + cmd_line)
        if options_storage.restart_from:
            updated_params = ""
            flag = False
            for v in args[1:]:
                if v == '-o' or v == '--restart-from':
                    flag = True
                    continue
                if flag:
                    flag = False
                    continue
                updated_params += " " + v
            updated_params = updated_params.strip()
            log.info("with updated parameters: " + updated_params)
            cmd_line += " " + updated_params
        log.info("")

    params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
    params_handler = logging.FileHandler(params_filename, mode='w')
    log.addHandler(params_handler)

    if options_storage.continue_mode:
        log.info(cmd_line)
    else:
        command = "Command line:"
        for v in args:
            command += " " + v
        log.info(command)

    # special case
    if "mismatch_corrector" in cfg and not support.get_lib_ids_by_type(dataset_data, 'paired-end'):
        support.warning('cannot perform mismatch correction without at least one paired-end library! Skipping this step.', log)
        del cfg["mismatch_corrector"]

    print_used_values(cfg, log)
    log.removeHandler(params_handler)

    if not options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline started. Log can be found here: " + log_filename + "\n")

    # splitting interlaced reads and processing Ns in additional contigs if needed
    if support.dataset_has_interlaced_reads(dataset_data) or support.dataset_has_additional_contigs(dataset_data):
        dir_for_split_reads = os.path.join(options_storage.output_dir, 'split_input')
        if support.dataset_has_interlaced_reads(dataset_data):
            if not os.path.isdir(dir_for_split_reads):
                os.makedirs(dir_for_split_reads)
            dataset_data = support.split_interlaced_reads(dataset_data, dir_for_split_reads, log)
        if support.dataset_has_additional_contigs(dataset_data):
            dataset_data = support.process_Ns_in_additional_contigs(dataset_data, dir_for_split_reads, log)
        options_storage.dataset_yaml_filename = os.path.join(options_storage.output_dir, "input_dataset.yaml")
        pyyaml.dump(dataset_data, open(options_storage.dataset_yaml_filename, 'w'))
        cfg["dataset"].yaml_filename = options_storage.dataset_yaml_filename

    try:
        # copying configs before all computations (to prevent its changing at run time)
        tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
        if os.path.isdir(tmp_configs_dir) and not options_storage.continue_mode:
            shutil.rmtree(tmp_configs_dir)
        if not os.path.isdir(tmp_configs_dir):
            dir_util.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False)

        corrected_dataset_yaml_filename = ''
        if "error_correction" in cfg:
            STAGE_NAME = "Read error correction"
            bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
            corrected_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "corrected.yaml")
            if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
                and not options_storage.restart_from == "ec":
                log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
            else:
                support.continue_from_here(log)

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in bh_cfg.__dict__:
                    os.environ["HEAPCHECK"] = bh_cfg.heap_check

                if os.path.exists(bh_cfg.output_dir):
                    shutil.rmtree(bh_cfg.output_dir)
                os.makedirs(bh_cfg.output_dir)

                if support.get_lib_ids_by_type(dataset_data, options_storage.LONG_READS_TYPES):
                    not_used_dataset_data = support.get_libs_by_type(dataset_data, options_storage.LONG_READS_TYPES)
                    to_correct_dataset_data = support.rm_libs_by_type(dataset_data, options_storage.LONG_READS_TYPES)
                    to_correct_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "to_correct.yaml")
                    pyyaml.dump(to_correct_dataset_data, open(to_correct_dataset_yaml_filename, 'w'))
                    bh_cfg.__dict__["dataset_yaml_filename"] = to_correct_dataset_yaml_filename
                else:
                    not_used_dataset_data = None
                    bh_cfg.__dict__["dataset_yaml_filename"] = cfg["dataset"].yaml_filename

                log.info("\n===== %s started. \n" % STAGE_NAME)
                hammer_logic.run_hammer(corrected_dataset_yaml_filename, tmp_configs_dir, bin_home, bh_cfg, not_used_dataset_data,
                    ext_python_modules_home, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)

        result_contigs_filename = os.path.join(cfg["common"].output_dir, "contigs.fasta")
        result_scaffolds_filename = os.path.join(cfg["common"].output_dir, "scaffolds.fasta")
        misc_dir = os.path.join(cfg["common"].output_dir, "misc")
        ### if mismatch correction is enabled then result contigs are copied to misc directory
        assembled_contigs_filename = os.path.join(misc_dir, "assembled_contigs.fasta")
        assembled_scaffolds_filename = os.path.join(misc_dir, "assembled_scaffolds.fasta")
        if "assembly" in cfg:
            STAGE_NAME = "Assembling"
            spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
            spades_cfg.__dict__["result_contigs"] = result_contigs_filename
            spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename

            if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
                                                  or ("mismatch_corrector" in cfg and
                                                      os.path.isfile(assembled_contigs_filename)))\
                and not options_storage.restart_from == 'as' \
                and not (options_storage.restart_from and options_storage.restart_from.startswith('k')):

                log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                # calculating latest_dir for the next stages
                latest_dir = support.get_latest_dir(os.path.join(spades_cfg.output_dir, "K*"))
                if not latest_dir:
                    support.error("failed to continue the previous run! Please restart from previous stages or from the beginning.", log)
            else:
                old_result_files = [result_contigs_filename, result_scaffolds_filename,
                                    assembled_contigs_filename, assembled_scaffolds_filename]
                for format in [".fasta", ".fastg"]:
                    for old_result_file in old_result_files:
                        if os.path.isfile(old_result_file[:-6] + format):
                            os.remove(old_result_file[:-6] + format)

                if options_storage.restart_from == 'as':
                    support.continue_from_here(log)

                if os.path.isfile(corrected_dataset_yaml_filename):
                    dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
                    dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))
                if spades_cfg.disable_rr:
                    spades_cfg.__dict__["rr_enable"] = False
                else:
                    spades_cfg.__dict__["rr_enable"] = True

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in spades_cfg.__dict__:
                    os.environ["HEAPCHECK"] = spades_cfg.heap_check

                log.info("\n===== %s started.\n" % STAGE_NAME)

                # creating dataset
                dataset_filename = os.path.join(spades_cfg.output_dir, "dataset.info")
                if not os.path.isfile(dataset_filename) or not options_storage.continue_mode:
                    dataset_file = open(dataset_filename, 'w')
                    import process_cfg
                    dataset_file.write("single_cell" + '\t' + process_cfg.bool_to_str(cfg["dataset"].single_cell) + '\n')
                    if os.path.isfile(corrected_dataset_yaml_filename):
                        dataset_file.write("reads" + '\t' + process_cfg.process_spaces(corrected_dataset_yaml_filename) + '\n')
                    else:
                        dataset_file.write("reads" + '\t' + process_cfg.process_spaces(cfg["dataset"].yaml_filename) + '\n')
                    if spades_cfg.developer_mode and "reference" in cfg["dataset"].__dict__:
                        dataset_file.write("reference_genome" + '\t')
                        dataset_file.write(process_cfg.process_spaces(cfg["dataset"].reference) + '\n')
                    dataset_file.close()
                spades_cfg.__dict__["dataset"] = dataset_filename

                latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home, spades_cfg, dataset_data, ext_python_modules_home, log)

                if os.path.isdir(misc_dir) and not options_storage.continue_mode:
                    shutil.rmtree(misc_dir)
                if not os.path.isdir(misc_dir):
                    os.makedirs(misc_dir)

                if options_storage.continue_mode and options_storage.restart_from and options_storage.restart_from.startswith('k'):
                    k_str = options_storage.restart_from[1:]
                    if k_str.find(":") != -1:
                        k_str = k_str[:k_str.find(":")]
                    support.error("failed to continue from K=%s because this K was not processed in the original run!" % k_str, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)

            #corrector
            if "mismatch_corrector" in cfg and (os.path.isfile(result_contigs_filename) or
                                                (options_storage.continue_mode and os.path.isfile(assembled_contigs_filename))):
                STAGE_NAME = "Mismatch correction"
                to_correct = dict()
                to_correct["contigs"] = (result_contigs_filename, assembled_contigs_filename)
                if os.path.isfile(result_scaffolds_filename) or (options_storage.continue_mode and
                                                                 os.path.isfile(assembled_scaffolds_filename)):
                    to_correct["scaffolds"] = (result_scaffolds_filename, assembled_scaffolds_filename)

                # moving assembled contigs (scaffolds) to misc dir
                for assembly_type, (old, new) in to_correct.items():
                    if options_storage.continue_mode and os.path.isfile(new):
                        continue
                    for format in [".fasta", ".fastg"]:
                        if os.path.isfile(old[:-6] + format):
                            shutil.move(old[:-6] + format, new[:-6] + format)

                if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
                    (os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)) \
                    and not options_storage.restart_from == 'mc':
                    log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                else:
                    if options_storage.restart_from == 'mc':
                        support.continue_from_here(log)

                    log.info("\n===== %s started." % STAGE_NAME)
                    # detecting paired-end library with the largest insert size
                    est_params_data = pyyaml.load(open(os.path.join(latest_dir, "final.lib_data"), 'r'))
                    max_IS_library = None
                    for reads_library in est_params_data:
                        if reads_library['type'] == 'paired-end':
                            if not max_IS_library or float(reads_library["insert size mean"]) > float(max_IS_library["insert size mean"]):
                                max_IS_library = reads_library
                    if not max_IS_library:
                        support.error('Mismatch correction cannot be performed without at least one paired-end library!', log)
                    if not max_IS_library["insert size mean"]:
                        support.warning('Failed to estimate insert size for all paired-end libraries. Starting Mismatch correction'
                                        ' based on the first paired-end library and with default insert size.', log)
                    else:
                        cfg["mismatch_corrector"].__dict__["insert-size"] = round(max_IS_library["insert size mean"])
                    yaml_dirname = os.path.dirname(options_storage.dataset_yaml_filename)
                    cfg["mismatch_corrector"].__dict__["1"] = list(map(lambda x: os.path.join(yaml_dirname, x),
                        max_IS_library['left reads']))
                    cfg["mismatch_corrector"].__dict__["2"] = list(map(lambda x: os.path.join(yaml_dirname, x),
                        max_IS_library['right reads']))
                    #TODO: add reads orientation

                    import corrector
                    corrector_cfg = cfg["mismatch_corrector"]
                    args = []
                    for key, values in corrector_cfg.__dict__.items():
                        if key == "output-dir":
                            continue

                        # for processing list of reads
                        if not isinstance(values, list):
                            values = [values]
                        for value in values:
                            if len(key) == 1:
                                args.append('-' + key)
                            else:
                                args.append('--' + key)
                            if value is not None:
                                args.append(value)

                    # processing contigs and scaffolds (or only contigs)
                    for assembly_type, (corrected, assembled) in to_correct.items():
                        if options_storage.continue_mode and os.path.isfile(corrected):
                            log.info("\n== Skipping processing of " + assembly_type + " (already processed)\n")
                            continue

                        support.continue_from_here(log)
                        log.info("\n== Processing of " + assembly_type + "\n")

                        cur_args = args[:]
                        cur_args += ['-c', assembled]
                        tmp_dir_for_corrector = support.get_tmp_dir(prefix="mis_cor_%s_" % assembly_type)
                        cur_args += ['--output-dir', tmp_dir_for_corrector]

                        # correcting
                        corrector.main(cur_args, ext_python_modules_home, log)

                        result_corrected_filename = os.path.join(tmp_dir_for_corrector, "corrected_contigs.fasta")
                        # moving corrected contigs (scaffolds) to SPAdes output dir
                        if os.path.isfile(result_corrected_filename):
                            shutil.move(result_corrected_filename, corrected)

                        if os.path.isdir(tmp_dir_for_corrector):
                            shutil.rmtree(tmp_dir_for_corrector)

                        assembled_fastg = assembled[:-6] + ".fastg"
                        if os.path.isfile(assembled_fastg):
                            support.create_fastg_from_fasta(corrected, assembled_fastg, log)
                    log.info("\n===== %s finished.\n" % STAGE_NAME)

        if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
            shutil.rmtree(tmp_configs_dir)

        #log.info("")
        if "error_correction" in cfg and os.path.isdir(os.path.dirname(corrected_dataset_yaml_filename)):
            log.info(" * Corrected reads are in " + support.process_spaces(os.path.dirname(corrected_dataset_yaml_filename) + "/"))
        if "assembly" in cfg and os.path.isfile(result_contigs_filename):
            message = " * Assembled contigs are in " + support.process_spaces(result_contigs_filename)
            if os.path.isfile(result_contigs_filename[:-6] + ".fastg"):
                message += " (" + os.path.basename(result_contigs_filename[:-6] + ".fastg") + ")"
            log.info(message)
        if "assembly" in cfg and os.path.isfile(result_scaffolds_filename):
            message = " * Assembled scaffolds are in " + support.process_spaces(result_scaffolds_filename)
            if os.path.isfile(result_scaffolds_filename[:-6] + ".fastg"):
                message += " (" + os.path.basename(result_scaffolds_filename[:-6] + ".fastg") + ")"
            log.info(message)
        #log.info("")

        #breaking scaffolds
        if os.path.isfile(result_scaffolds_filename):
            if not os.path.isdir(misc_dir):
                os.makedirs(misc_dir)
            result_broken_scaffolds = os.path.join(misc_dir, "broken_scaffolds.fasta")
            if not os.path.isfile(result_broken_scaffolds) or not options_storage.continue_mode:
                modified, broken_scaffolds = support.break_scaffolds(result_scaffolds_filename,
                    options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)
                if modified:
                    support.write_fasta(result_broken_scaffolds, broken_scaffolds)
                    #log.info(" * Scaffolds broken by " + str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS) +
                    # " Ns are in " + result_broken_scaffolds)

        ### printing WARNINGS SUMMARY
        if not support.log_warnings(log):
            log.info("\n======= SPAdes pipeline finished.")  # otherwise it finished WITH WARNINGS

        if options_storage.test_mode:
            for result_filename in [result_contigs_filename, result_scaffolds_filename]:
                if os.path.isfile(result_filename):
                    result_fasta = list(support.read_fasta(result_filename))
                    # correctness check: should be one contig of length 1000 bp
                    correct_number = 1
                    correct_length = 1000
                    if not len(result_fasta):
                        support.error("TEST FAILED: %s does not contain contigs!" % result_filename)
                    elif len(result_fasta) > correct_number:
                        support.error("TEST FAILED: %s contains more than %d contig (%d)!" %
                                      (result_filename, correct_number, len(result_fasta)))
                    elif len(result_fasta[0][1]) != correct_length:
                        if len(result_fasta[0][1]) > correct_length:
                            relation = "more"
                        else:
                            relation = "less"
                        support.error("TEST FAILED: %s contains %s than %d bp (%d bp)!" %
                                      (result_filename, relation, correct_length, len(result_fasta[0][1])))
                else:
                    support.error("TEST FAILED: " + result_filename + " does not exist!")
            log.info("\n========= TEST PASSED CORRECTLY.")


        log.info("\nSPAdes log can be found here: " + log_filename)
        log.info("")
        log.info("Thank you for using SPAdes!")
        log.removeHandler(log_handler)

    except Exception:
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            if exc_type == OSError and exc_value.errno == errno.ENOEXEC: # Exec format error
                support.error("It looks like you are using SPAdes binaries for another platform.\n" +
                              support.get_spades_binaries_info_message())
            else:
                log.exception(exc_value)
                support.error("exception caught: %s" % exc_type, log)
    except BaseException: # since python 2.5 system-exiting exceptions (e.g. KeyboardInterrupt) are derived from BaseException
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            log.exception(exc_value)
            support.error("exception caught: %s" % exc_type, log)
def main(args):
    os.environ["LC_ALL"] = "C"

    if len(args) == 1:
        show_usage(0)

    log = logging.getLogger('spades')
    log.setLevel(logging.DEBUG)

    console = logging.StreamHandler(sys.stdout)
    console.setFormatter(logging.Formatter('%(message)s'))
    console.setLevel(logging.DEBUG)
    log.addHandler(console)

    support.check_binaries(bin_home, log)

    # parse options and safe all parameters to cfg
    options = args
    cfg, dataset_data = fill_cfg(options, log)

    if options_storage.continue_mode:
        cmd_line, options = get_options_from_params(os.path.join(options_storage.output_dir, "params.txt"), args[0])
        if not options:
            support.error("failed to parse command line of the previous run! Please restart from the beginning or specify another output directory.")
        cfg, dataset_data = fill_cfg(options, log, secondary_filling=True)
        if options_storage.restart_from:
            check_cfg_for_partial_run(cfg, type='restart-from')
        options_storage.continue_mode = True
    if options_storage.stop_after:
        check_cfg_for_partial_run(cfg, type='stop-after')

    log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
    if options_storage.continue_mode:
        log_handler = logging.FileHandler(log_filename, mode='a')
    else:
        log_handler = logging.FileHandler(log_filename, mode='w')
    log.addHandler(log_handler)

    if options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline continued. Log can be found here: " + log_filename + "\n")
        log.info("Restored from " + cmd_line)
        if options_storage.restart_from:
            updated_params = ""
            skip_next = False
            for v in args[1:]:
                if v == '-o' or v == '--restart-from':
                    skip_next = True
                    continue
                if skip_next or v.startswith('--restart-from='):  # you can specify '--restart-from=k33' but not '-o=out_dir'
                    skip_next = False
                    continue
                updated_params += " " + v
            updated_params = updated_params.strip()
            log.info("with updated parameters: " + updated_params)
            cmd_line += " " + updated_params
        log.info("")

    params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
    params_handler = logging.FileHandler(params_filename, mode='w')
    log.addHandler(params_handler)

    if options_storage.continue_mode:
        log.info(cmd_line)
    else:
        command = "Command line: "
        for v in args:
            # substituting relative paths with absolute ones (read paths, output dir path, etc)
            v, prefix = support.get_option_prefix(v)
            if v in options_storage.dict_of_rel2abs.keys():
                v = options_storage.dict_of_rel2abs[v]
            if prefix:
                command += prefix + ":"
            command += v + " "
        log.info(command)

    # special case
#    if "mismatch_corrector" in cfg and not support.get_lib_ids_by_type(dataset_data, 'paired-end'):
#        support.warning('cannot perform mismatch correction without at least one paired-end library! Skipping this step.', log)
#        del cfg["mismatch_corrector"]

    print_used_values(cfg, log)
    log.removeHandler(params_handler)

    support.check_single_reads_in_options(options, log)

    if not options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline started. Log can be found here: " + log_filename + "\n")

    # splitting interlaced reads and processing Ns in additional contigs if needed
    if support.dataset_has_interlaced_reads(dataset_data) or support.dataset_has_additional_contigs(dataset_data)\
            or support.dataset_has_nxmate_reads(dataset_data):
        dir_for_split_reads = os.path.join(options_storage.output_dir, 'split_input')
        if support.dataset_has_interlaced_reads(dataset_data) or support.dataset_has_nxmate_reads(dataset_data):
            if not os.path.isdir(dir_for_split_reads):
                os.makedirs(dir_for_split_reads)
            if support.dataset_has_interlaced_reads(dataset_data):
                dataset_data = support.split_interlaced_reads(dataset_data, dir_for_split_reads, log)
            if support.dataset_has_nxmate_reads(dataset_data):
                dataset_data = support.process_nxmate_reads(dataset_data, dir_for_split_reads, log)
        if support.dataset_has_additional_contigs(dataset_data):
            dataset_data = support.process_Ns_in_additional_contigs(dataset_data, dir_for_split_reads, log)
        options_storage.dataset_yaml_filename = os.path.join(options_storage.output_dir, "input_dataset.yaml")
        pyyaml.dump(dataset_data, open(options_storage.dataset_yaml_filename, 'w'))
        cfg["dataset"].yaml_filename = options_storage.dataset_yaml_filename

    try:
        # copying configs before all computations (to prevent its changing at run time)
        tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
        if os.path.isdir(tmp_configs_dir) and not options_storage.continue_mode:
            shutil.rmtree(tmp_configs_dir)
        if not os.path.isdir(tmp_configs_dir):
            if options_storage.configs_dir:
                dir_util.copy_tree(options_storage.configs_dir, tmp_configs_dir, preserve_times=False)
            else:
                dir_util.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False)

        corrected_dataset_yaml_filename = ''
        if "error_correction" in cfg:
            STAGE_NAME = "Read error correction"
            bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
            corrected_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "corrected.yaml")
            if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
                and not options_storage.restart_from == "ec":
                log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
            else:
                support.continue_from_here(log)

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in bh_cfg.__dict__:
                    os.environ["HEAPCHECK"] = bh_cfg.heap_check

                if os.path.exists(bh_cfg.output_dir):
                    shutil.rmtree(bh_cfg.output_dir)
                os.makedirs(bh_cfg.output_dir)

                if support.get_lib_ids_by_type(dataset_data, options_storage.LONG_READS_TYPES):
                    not_used_dataset_data = support.get_libs_by_type(dataset_data, options_storage.LONG_READS_TYPES)
                    to_correct_dataset_data = support.rm_libs_by_type(dataset_data, options_storage.LONG_READS_TYPES)
                    to_correct_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "to_correct.yaml")
                    pyyaml.dump(to_correct_dataset_data, open(to_correct_dataset_yaml_filename, 'w'))
                    bh_cfg.__dict__["dataset_yaml_filename"] = to_correct_dataset_yaml_filename
                else:
                    not_used_dataset_data = None
                    bh_cfg.__dict__["dataset_yaml_filename"] = cfg["dataset"].yaml_filename

                log.info("\n===== %s started. \n" % STAGE_NAME)

                hammer_logic.run_hammer(corrected_dataset_yaml_filename, tmp_configs_dir, bin_home, bh_cfg, not_used_dataset_data,
                    ext_python_modules_home, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)
            if options_storage.stop_after == 'ec':
                support.finish_here(log)

        result_contigs_filename = os.path.join(cfg["common"].output_dir, "contigs.fasta")
        result_scaffolds_filename = os.path.join(cfg["common"].output_dir, "scaffolds.fasta")
        result_assembly_graph_filename = os.path.join(cfg["common"].output_dir, "assembly_graph.fastg")
        truseq_long_reads_file_base = os.path.join(cfg["common"].output_dir, "truseq_long_reads")
        truseq_long_reads_file = truseq_long_reads_file_base + ".fasta"
        misc_dir = os.path.join(cfg["common"].output_dir, "misc")
        ### if mismatch correction is enabled then result contigs are copied to misc directory
        assembled_contigs_filename = os.path.join(misc_dir, "assembled_contigs.fasta")
        assembled_scaffolds_filename = os.path.join(misc_dir, "assembled_scaffolds.fasta")
        if "assembly" in cfg and not options_storage.run_completed:
            STAGE_NAME = "Assembling"
            spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
            spades_cfg.__dict__["result_contigs"] = result_contigs_filename
            spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename
            spades_cfg.__dict__["result_graph"] = result_assembly_graph_filename

            if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
                                                  or ("mismatch_corrector" in cfg and
                                                      os.path.isfile(assembled_contigs_filename)))\
                and not options_storage.restart_from == 'as' \
                and not options_storage.restart_from == 'scc' \
                and not (options_storage.restart_from and options_storage.restart_from.startswith('k')):

                log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                # calculating latest_dir for the next stages
                latest_dir = support.get_latest_dir(os.path.join(spades_cfg.output_dir, "K*"))
                if not latest_dir:
                    support.error("failed to continue the previous run! Please restart from previous stages or from the beginning.", log)
            else:
                old_result_files = [result_contigs_filename, result_scaffolds_filename,
                                    assembled_contigs_filename, assembled_scaffolds_filename]
                for old_result_file in old_result_files:
                    if os.path.isfile(old_result_file):
                        os.remove(old_result_file)

                if options_storage.restart_from == 'as':
                    support.continue_from_here(log)

                if os.path.isfile(corrected_dataset_yaml_filename):
                    dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
                    dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))
                if spades_cfg.disable_rr:
                    spades_cfg.__dict__["rr_enable"] = False
                else:
                    spades_cfg.__dict__["rr_enable"] = True

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in spades_cfg.__dict__:
                    os.environ["HEAPCHECK"] = spades_cfg.heap_check

                log.info("\n===== %s started.\n" % STAGE_NAME)

                # creating dataset
                dataset_filename = os.path.join(spades_cfg.output_dir, "dataset.info")
                if not os.path.isfile(dataset_filename) or not options_storage.continue_mode:
                    dataset_file = open(dataset_filename, 'w')
                    import process_cfg
                    dataset_file.write("single_cell" + '\t' + process_cfg.bool_to_str(cfg["dataset"].single_cell) + '\n')
                    dataset_file.write("meta" + '\t' + process_cfg.bool_to_str(cfg["dataset"].meta) + '\n')
                    dataset_file.write("moleculo" + '\t' + process_cfg.bool_to_str(cfg["dataset"].truseq) + '\n')
                    if os.path.isfile(corrected_dataset_yaml_filename):
                        dataset_file.write("reads" + '\t' + process_cfg.process_spaces(corrected_dataset_yaml_filename) + '\n')
                    else:
                        dataset_file.write("reads" + '\t' + process_cfg.process_spaces(cfg["dataset"].yaml_filename) + '\n')
                    if spades_cfg.developer_mode and "reference" in cfg["dataset"].__dict__:
                        dataset_file.write("reference_genome" + '\t')
                        dataset_file.write(process_cfg.process_spaces(cfg["dataset"].reference) + '\n')
                    dataset_file.close()
                spades_cfg.__dict__["dataset"] = dataset_filename

                latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home, spades_cfg, dataset_data, ext_python_modules_home, log)

                if os.path.isdir(misc_dir) and not options_storage.continue_mode:
                    shutil.rmtree(misc_dir)
                if not os.path.isdir(misc_dir):
                    os.makedirs(misc_dir)

                if options_storage.continue_mode and options_storage.restart_from and options_storage.restart_from.startswith('k'):
                    k_str = options_storage.restart_from[1:]
                    if k_str.find(":") != -1:
                        k_str = k_str[:k_str.find(":")]
                    support.error("failed to continue from K=%s because this K was not processed in the original run!" % k_str, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)
            if not options_storage.run_completed:
                if options_storage.stop_after == 'as' or options_storage.stop_after == 'scc' or (options_storage.stop_after and options_storage.stop_after.startswith('k')):
                    support.finish_here(log)

            #postprocessing
            if cfg["run_truseq_postprocessing"] and not options_storage.run_completed:
                if options_storage.continue_mode and os.path.isfile(truseq_long_reads_file_base + ".fastq") and not options_storage.restart_from == 'tpp':
                    log.info("\n===== Skipping %s (already processed). \n" % "TruSeq postprocessing")
                else:
                    support.continue_from_here(log)
                    if os.path.isfile(result_scaffolds_filename):
                        shutil.move(result_scaffolds_filename, assembled_scaffolds_filename)
                    reads_library = dataset_data[0]
                    alignment_bin = os.path.join(bin_home, "bwa-spades")
                    alignment_dir = os.path.join(cfg["common"].output_dir, "alignment")
                    sam_files = alignment.align_bwa(alignment_bin, assembled_scaffolds_filename, dataset_data, alignment_dir, log, options_storage.threads)
                    moleculo_postprocessing.moleculo_postprocessing(assembled_scaffolds_filename, truseq_long_reads_file_base, sam_files, log)
                if options_storage.stop_after == 'tpp':
                    support.finish_here(log)

            #corrector
            if "mismatch_corrector" in cfg and not options_storage.run_completed and \
                    (os.path.isfile(result_contigs_filename) or
                    (options_storage.continue_mode and os.path.isfile(assembled_contigs_filename))):
                STAGE_NAME = "Mismatch correction"
                to_correct = dict()
                to_correct["contigs"] = (result_contigs_filename, assembled_contigs_filename)
                if os.path.isfile(result_scaffolds_filename) or (options_storage.continue_mode and
                                                                 os.path.isfile(assembled_scaffolds_filename)):
                    to_correct["scaffolds"] = (result_scaffolds_filename, assembled_scaffolds_filename)

                # moving assembled contigs (scaffolds) to misc dir
                for assembly_type, (old, new) in to_correct.items():
                    if options_storage.continue_mode and os.path.isfile(new):
                        continue
                    if os.path.isfile(old):
                        shutil.move(old, new)

                if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
                    (os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)) \
                    and not options_storage.restart_from == 'mc':
                    log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                else:
                    if options_storage.restart_from == 'mc':
                        support.continue_from_here(log)

                    log.info("\n===== %s started." % STAGE_NAME)
                    # detecting paired-end library with the largest insert size
                    cfg["mismatch_corrector"].__dict__["dataset"] = cfg["dataset"].yaml_filename
                    #TODO: add reads orientation

                    import corrector_logic
                    corrector_cfg = cfg["mismatch_corrector"]
                    # processing contigs and scaffolds (or only contigs)
                    for assembly_type, (corrected, assembled) in to_correct.items():
                        if options_storage.continue_mode and os.path.isfile(corrected):
                            log.info("\n== Skipping processing of " + assembly_type + " (already processed)\n")
                            continue

                        support.continue_from_here(log)
                        log.info("\n== Processing of " + assembly_type + "\n")

                        tmp_dir_for_corrector = os.path.join(cfg["common"].output_dir, "mismatch_corrector", assembly_type)

                        cfg["mismatch_corrector"].__dict__["output_dir"] = tmp_dir_for_corrector
                        # correcting
                        corr_cfg = merge_configs(cfg["mismatch_corrector"], cfg["common"])
                        
                        result_corrected_filename = os.path.join(tmp_dir_for_corrector, "corrected_contigs.fasta")

                        corrector_logic.run_corrector( tmp_configs_dir, bin_home, corr_cfg,
                        ext_python_modules_home, log, assembled, result_corrected_filename)

                        if os.path.isfile(result_corrected_filename):
                            shutil.copyfile(result_corrected_filename, corrected)
                        tmp_d = os.path.join(tmp_dir_for_corrector, "tmp")
                        if os.path.isdir(tmp_d) and not cfg["common"].developer_mode:
                            shutil.rmtree(tmp_d)
                    log.info("\n===== %s finished.\n" % STAGE_NAME)
                if options_storage.stop_after == 'mc':
                    support.finish_here(log)

        if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
            shutil.rmtree(tmp_configs_dir)

        if not options_storage.run_completed:
            #log.info("")
            if "error_correction" in cfg and os.path.isdir(os.path.dirname(corrected_dataset_yaml_filename)):
                log.info(" * Corrected reads are in " + support.process_spaces(os.path.dirname(corrected_dataset_yaml_filename) + "/"))
            if "assembly" in cfg and os.path.isfile(result_contigs_filename):
                message = " * Assembled contigs are in " + support.process_spaces(result_contigs_filename)
                log.info(message)
            if "assembly" in cfg and os.path.isfile(result_scaffolds_filename):
                message = " * Assembled scaffolds are in " + support.process_spaces(result_scaffolds_filename)
                log.info(message)
            if "assembly" in cfg and os.path.isfile(result_assembly_graph_filename):
                message = " * Assembly graph is in " + support.process_spaces(result_assembly_graph_filename)
                log.info(message)
            #log.info("")

        #breaking scaffolds
        if os.path.isfile(result_scaffolds_filename):
            if not os.path.isdir(misc_dir):
                os.makedirs(misc_dir)
            result_broken_scaffolds = os.path.join(misc_dir, "broken_scaffolds.fasta")
            if not os.path.isfile(result_broken_scaffolds) or not options_storage.continue_mode:
                modified, broken_scaffolds = support.break_scaffolds(result_scaffolds_filename,
                    options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)
                if modified:
                    support.write_fasta(result_broken_scaffolds, broken_scaffolds)
                    #log.info(" * Scaffolds broken by " + str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS) +
                    # " Ns are in " + result_broken_scaffolds)

        ### printing WARNINGS SUMMARY
        if not support.log_warnings(log):
            log.info("\n======= SPAdes pipeline finished.")  # otherwise it finished WITH WARNINGS

        if options_storage.test_mode:
            if options_storage.truseq_mode:
                if not os.path.isfile(truseq_long_reads_file):
                    support.error("TEST FAILED: %s does not exist!" % truseq_long_reads_file)
            else:
                for result_filename in [result_contigs_filename, result_scaffolds_filename]:
                    if os.path.isfile(result_filename):
                        result_fasta = list(support.read_fasta(result_filename))
                        # correctness check: should be one contig of length 1000 bp
                        correct_number = 1
                        correct_length = 1000
                        if not len(result_fasta):
                            support.error("TEST FAILED: %s does not contain contigs!" % result_filename)
                        elif len(result_fasta) > correct_number:
                            support.error("TEST FAILED: %s contains more than %d contig (%d)!" %
                                          (result_filename, correct_number, len(result_fasta)))
                        elif len(result_fasta[0][1]) != correct_length:
                            if len(result_fasta[0][1]) > correct_length:
                                relation = "more"
                            else:
                                relation = "less"
                            support.error("TEST FAILED: %s contains %s than %d bp (%d bp)!" %
                                          (result_filename, relation, correct_length, len(result_fasta[0][1])))
                    else:
                        support.error("TEST FAILED: " + result_filename + " does not exist!")
            log.info("\n========= TEST PASSED CORRECTLY.")


        log.info("\nSPAdes log can be found here: " + log_filename)
        log.info("")
        log.info("Thank you for using SPAdes!")
        log.removeHandler(log_handler)

    except Exception:
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            if exc_type == OSError and exc_value.errno == errno.ENOEXEC: # Exec format error
                support.error("It looks like you are using SPAdes binaries for another platform.\n" +
                              support.get_spades_binaries_info_message())
            else:
                log.exception(exc_value)
                support.error("exception caught: %s" % exc_type, log)
    except BaseException:  # since python 2.5 system-exiting exceptions (e.g. KeyboardInterrupt) are derived from BaseException
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            log.exception(exc_value)
            support.error("exception caught: %s" % exc_type, log)
Example #4
0
def main(args):
    os.environ["LC_ALL"] = "C"

    if len(args) == 1:
        show_usage(0)

    log = logging.getLogger('spades')
    log.setLevel(logging.DEBUG)

    console = logging.StreamHandler(sys.stdout)
    console.setFormatter(logging.Formatter('%(message)s'))
    console.setLevel(logging.DEBUG)
    log.addHandler(console)

    support.check_binaries(bin_home, log)

    # auto detecting SPAdes mode (rna, meta, etc)
    mode = options_storage.get_mode()
    if mode is not None:
        args.append('--' + mode)

    # parse options and safe all parameters to cfg
    options = args
    cfg, dataset_data = fill_cfg(options, log)

    if options_storage.continue_mode:
        cmd_line, options = get_options_from_params(os.path.join(options_storage.output_dir, "params.txt"), args[0])
        if not options:
            support.error("failed to parse command line of the previous run! Please restart from the beginning or specify another output directory.")
        cfg, dataset_data = fill_cfg(options, log, secondary_filling=True)
        if options_storage.restart_from:
            check_cfg_for_partial_run(cfg, type='restart-from')
        options_storage.continue_mode = True
    if options_storage.stop_after:
        check_cfg_for_partial_run(cfg, type='stop-after')

    log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
    if options_storage.continue_mode:
        log_handler = logging.FileHandler(log_filename, mode='a')
    else:
        log_handler = logging.FileHandler(log_filename, mode='w')
    log.addHandler(log_handler)

    if options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline continued. Log can be found here: " + log_filename + "\n")
        log.info("Restored from " + cmd_line)
        if options_storage.restart_from:
            updated_params = ""
            skip_next = False
            for v in args[1:]:
                if v == '-o' or v == '--restart-from':
                    skip_next = True
                    continue
                if skip_next or v.startswith('--restart-from='):  # you can specify '--restart-from=k33' but not '-o=out_dir'
                    skip_next = False
                    continue
                updated_params += "\t" + v
            updated_params = updated_params.strip()
            log.info("with updated parameters: " + updated_params)
            cmd_line += "\t" + updated_params
        log.info("")

    params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
    params_handler = logging.FileHandler(params_filename, mode='w')
    log.addHandler(params_handler)

    if options_storage.continue_mode:
        log.info(cmd_line)
    else:
        command = "Command line: "
        for v in args:
            # substituting relative paths with absolute ones (read paths, output dir path, etc)
            v, prefix = support.get_option_prefix(v)
            if v in options_storage.dict_of_rel2abs.keys():
                v = options_storage.dict_of_rel2abs[v]
            if prefix:
                command += prefix + ":"
            command += v + "\t"
        log.info(command)

    # special case
#    if "mismatch_corrector" in cfg and not support.get_lib_ids_by_type(dataset_data, 'paired-end'):
#        support.warning('cannot perform mismatch correction without at least one paired-end library! Skipping this step.', log)
#        del cfg["mismatch_corrector"]

    print_used_values(cfg, log)
    log.removeHandler(params_handler)

    support.check_single_reads_in_options(options, log)

    if not options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline started. Log can be found here: " + log_filename + "\n")

    # splitting interlaced reads and processing Ns in additional contigs if needed
    if support.dataset_has_interlaced_reads(dataset_data) or support.dataset_has_additional_contigs(dataset_data)\
            or support.dataset_has_nxmate_reads(dataset_data):
        dir_for_split_reads = os.path.join(options_storage.output_dir, 'split_input')
        if support.dataset_has_interlaced_reads(dataset_data) or support.dataset_has_nxmate_reads(dataset_data):
            if not os.path.isdir(dir_for_split_reads):
                os.makedirs(dir_for_split_reads)
            if support.dataset_has_interlaced_reads(dataset_data):
                dataset_data = support.split_interlaced_reads(dataset_data, dir_for_split_reads, log)
            if support.dataset_has_nxmate_reads(dataset_data):
                dataset_data = support.process_nxmate_reads(dataset_data, dir_for_split_reads, log)
        if support.dataset_has_additional_contigs(dataset_data):
            dataset_data = support.process_Ns_in_additional_contigs(dataset_data, dir_for_split_reads, log)
        options_storage.dataset_yaml_filename = os.path.join(options_storage.output_dir, "input_dataset.yaml")
        pyyaml.dump(dataset_data, open(options_storage.dataset_yaml_filename, 'w'))
        cfg["dataset"].yaml_filename = options_storage.dataset_yaml_filename

    try:
        # copying configs before all computations (to prevent its changing at run time)
        tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
        if os.path.isdir(tmp_configs_dir) and not options_storage.continue_mode:
            shutil.rmtree(tmp_configs_dir)
        if not os.path.isdir(tmp_configs_dir):
            if options_storage.configs_dir:
                dir_util.copy_tree(options_storage.configs_dir, tmp_configs_dir, preserve_times=False, preserve_mode=False)
            else:
                dir_util.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False, preserve_mode=False)

        corrected_dataset_yaml_filename = ''
        if "error_correction" in cfg:
            STAGE_NAME = "Read error correction"
            bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
            corrected_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "corrected.yaml")
            ec_is_needed = True
            only_compressing_is_needed = False
            if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
                    and not options_storage.restart_from == "ec":
                if not bh_cfg.gzip_output or \
                        support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))):
                    log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                    ec_is_needed = False
                else:
                    only_compressing_is_needed = True
            if ec_is_needed:
                if not only_compressing_is_needed:
                    support.continue_from_here(log)

                    if "HEAPCHECK" in os.environ:
                        del os.environ["HEAPCHECK"]
                    if "heap_check" in bh_cfg.__dict__:
                        os.environ["HEAPCHECK"] = bh_cfg.heap_check

                    if os.path.exists(bh_cfg.output_dir):
                        shutil.rmtree(bh_cfg.output_dir)
                    os.makedirs(bh_cfg.output_dir)

                bh_cfg.__dict__["dataset_yaml_filename"] = cfg["dataset"].yaml_filename
                log.info("\n===== %s started. \n" % STAGE_NAME)

                hammer_logic.run_hammer(corrected_dataset_yaml_filename, tmp_configs_dir, bin_home, bh_cfg, dataset_data,
                    ext_python_modules_home, only_compressing_is_needed, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)
            if options_storage.stop_after == 'ec':
                support.finish_here(log)

        result_contigs_filename = os.path.join(cfg["common"].output_dir, options_storage.contigs_name)
        result_scaffolds_filename = os.path.join(cfg["common"].output_dir, options_storage.scaffolds_name)
        result_assembly_graph_filename = os.path.join(cfg["common"].output_dir, options_storage.assembly_graph_name)
        result_contigs_paths_filename = os.path.join(cfg["common"].output_dir, options_storage.contigs_paths)
        result_scaffolds_paths_filename = os.path.join(cfg["common"].output_dir, options_storage.scaffolds_paths)
        result_transcripts_filename = os.path.join(cfg["common"].output_dir, options_storage.transcripts_name)
        result_transcripts_paths_filename = os.path.join(cfg["common"].output_dir, options_storage.transcripts_paths)
        truseq_long_reads_file_base = os.path.join(cfg["common"].output_dir, "truseq_long_reads")
        truseq_long_reads_file = truseq_long_reads_file_base + ".fasta"
        misc_dir = os.path.join(cfg["common"].output_dir, "misc")
        ### if mismatch correction is enabled then result contigs are copied to misc directory
        assembled_contigs_filename = os.path.join(misc_dir, "assembled_contigs.fasta")
        assembled_scaffolds_filename = os.path.join(misc_dir, "assembled_scaffolds.fasta")
        if "assembly" in cfg and not options_storage.run_completed:
            STAGE_NAME = "Assembling"
            spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
            spades_cfg.__dict__["result_contigs"] = result_contigs_filename
            spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename
            spades_cfg.__dict__["result_graph"] = result_assembly_graph_filename
            spades_cfg.__dict__["result_contigs_paths"] = result_contigs_paths_filename
            spades_cfg.__dict__["result_scaffolds_paths"] = result_scaffolds_paths_filename
            spades_cfg.__dict__["result_transcripts"] = result_transcripts_filename
            spades_cfg.__dict__["result_transcripts_paths"] = result_transcripts_paths_filename

            if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
                                                  or ("mismatch_corrector" in cfg and
                                                      os.path.isfile(assembled_contigs_filename))
                                                  or (options_storage.truseq_mode and os.path.isfile(assembled_scaffolds_filename)))\
                and not options_storage.restart_from == 'as' \
                and not options_storage.restart_from == 'scc' \
                and not (options_storage.restart_from and options_storage.restart_from.startswith('k')):

                log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                # calculating latest_dir for the next stages
                latest_dir = support.get_latest_dir(os.path.join(spades_cfg.output_dir, "K*"))
                if not latest_dir:
                    support.error("failed to continue the previous run! Please restart from previous stages or from the beginning.", log)
            else:
                old_result_files = [result_contigs_filename, result_scaffolds_filename,
                                    assembled_contigs_filename, assembled_scaffolds_filename]
                for old_result_file in old_result_files:
                    if os.path.isfile(old_result_file):
                        os.remove(old_result_file)

                if options_storage.restart_from == 'as':
                    support.continue_from_here(log)

                if os.path.isfile(corrected_dataset_yaml_filename):
                    dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
                    dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))
                if spades_cfg.disable_rr:
                    spades_cfg.__dict__["rr_enable"] = False
                else:
                    spades_cfg.__dict__["rr_enable"] = True

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in spades_cfg.__dict__:
                    os.environ["HEAPCHECK"] = spades_cfg.heap_check

                log.info("\n===== %s started.\n" % STAGE_NAME)

                # creating dataset
                dataset_filename = os.path.join(spades_cfg.output_dir, "dataset.info")
                if not os.path.isfile(dataset_filename) or not options_storage.continue_mode:
                    dataset_file = open(dataset_filename, 'w')
                    import process_cfg
                    if os.path.isfile(corrected_dataset_yaml_filename):
                        dataset_file.write("reads" + '\t' + process_cfg.process_spaces(corrected_dataset_yaml_filename) + '\n')
                    else:
                        dataset_file.write("reads" + '\t' + process_cfg.process_spaces(cfg["dataset"].yaml_filename) + '\n')
                    if spades_cfg.developer_mode and "reference" in cfg["dataset"].__dict__:
                        dataset_file.write("reference_genome" + '\t')
                        dataset_file.write(process_cfg.process_spaces(cfg["dataset"].reference) + '\n')
                    dataset_file.close()
                spades_cfg.__dict__["dataset"] = dataset_filename

                used_K = spades_logic.run_spades(tmp_configs_dir, bin_home, spades_cfg, dataset_data, ext_python_modules_home, log)

                if os.path.isdir(misc_dir) and not options_storage.continue_mode:
                    shutil.rmtree(misc_dir)
                if not os.path.isdir(misc_dir):
                    os.makedirs(misc_dir)

                if options_storage.continue_mode and options_storage.restart_from and options_storage.restart_from.startswith('k'):
                    k_str = options_storage.restart_from[1:]
                    if k_str.find(":") != -1:
                        k_str = k_str[:k_str.find(":")]
                    support.error("failed to continue from K=%s because this K was not processed in the original run!" % k_str, log)
                log.info("\n===== %s finished. Used k-mer sizes: %s \n" % (STAGE_NAME, ', '.join(map(str, used_K))))
            if not options_storage.run_completed:
                if options_storage.stop_after == 'as' or options_storage.stop_after == 'scc' or (options_storage.stop_after and options_storage.stop_after.startswith('k')):
                    support.finish_here(log)

            #postprocessing
            if cfg["run_truseq_postprocessing"] and not options_storage.run_completed:
                if options_storage.continue_mode and os.path.isfile(truseq_long_reads_file_base + ".fastq") and not options_storage.restart_from == 'tpp':
                    log.info("\n===== Skipping %s (already processed). \n" % "TruSeq postprocessing")
                else:
                    support.continue_from_here(log)
                    if os.path.isfile(result_scaffolds_filename):
                        shutil.move(result_scaffolds_filename, assembled_scaffolds_filename)
                    reads_library = dataset_data[0]
                    alignment_bin = os.path.join(bin_home, "bwa-spades")
                    alignment_dir = os.path.join(cfg["common"].output_dir, "alignment")
                    sam_files = alignment.align_bwa(alignment_bin, assembled_scaffolds_filename, dataset_data, alignment_dir, log, options_storage.threads)
                    moleculo_postprocessing.moleculo_postprocessing(assembled_scaffolds_filename, truseq_long_reads_file_base, sam_files, log)
                if options_storage.stop_after == 'tpp':
                    support.finish_here(log)

            #corrector
            if "mismatch_corrector" in cfg and not options_storage.run_completed and \
                    (os.path.isfile(result_contigs_filename) or
                    (options_storage.continue_mode and os.path.isfile(assembled_contigs_filename))):
                STAGE_NAME = "Mismatch correction"
                to_correct = dict()
                to_correct["contigs"] = (result_contigs_filename, assembled_contigs_filename)
                if os.path.isfile(result_scaffolds_filename) or (options_storage.continue_mode and
                                                                 os.path.isfile(assembled_scaffolds_filename)):
                    to_correct["scaffolds"] = (result_scaffolds_filename, assembled_scaffolds_filename)

                # moving assembled contigs (scaffolds) to misc dir
                for assembly_type, (old, new) in to_correct.items():
                    if options_storage.continue_mode and os.path.isfile(new):
                        continue
                    if os.path.isfile(old):
                        shutil.move(old, new)

                if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
                    (os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)) \
                    and not options_storage.restart_from == 'mc':
                    log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
                else:
                    if options_storage.restart_from == 'mc':
                        support.continue_from_here(log)

                    log.info("\n===== %s started." % STAGE_NAME)
                    # detecting paired-end library with the largest insert size
                    cfg["mismatch_corrector"].__dict__["dataset"] = cfg["dataset"].yaml_filename
                    #TODO: add reads orientation

                    import corrector_logic
                    corrector_cfg = cfg["mismatch_corrector"]
                    # processing contigs and scaffolds (or only contigs)
                    for assembly_type, (corrected, assembled) in to_correct.items():
                        if options_storage.continue_mode and os.path.isfile(corrected):
                            log.info("\n== Skipping processing of " + assembly_type + " (already processed)\n")
                            continue

                        support.continue_from_here(log)
                        log.info("\n== Processing of " + assembly_type + "\n")

                        tmp_dir_for_corrector = os.path.join(cfg["common"].output_dir, "mismatch_corrector", assembly_type)

                        cfg["mismatch_corrector"].__dict__["output_dir"] = tmp_dir_for_corrector
                        # correcting
                        corr_cfg = merge_configs(cfg["mismatch_corrector"], cfg["common"])
                        
                        result_corrected_filename = os.path.join(tmp_dir_for_corrector, "corrected_contigs.fasta")

                        corrector_logic.run_corrector( tmp_configs_dir, bin_home, corr_cfg,
                        ext_python_modules_home, log, assembled, result_corrected_filename)

                        if os.path.isfile(result_corrected_filename):
                            shutil.copyfile(result_corrected_filename, corrected)
                        tmp_d = os.path.join(tmp_dir_for_corrector, "tmp")
                        if os.path.isdir(tmp_d) and not cfg["common"].developer_mode:
                            shutil.rmtree(tmp_d)
                    log.info("\n===== %s finished.\n" % STAGE_NAME)
                if options_storage.stop_after == 'mc':
                    support.finish_here(log)

        if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
            shutil.rmtree(tmp_configs_dir)

        if not options_storage.run_completed:
            #log.info("")
            if "error_correction" in cfg and os.path.isdir(os.path.dirname(corrected_dataset_yaml_filename)):
                log.info(" * Corrected reads are in " + support.process_spaces(os.path.dirname(corrected_dataset_yaml_filename) + "/"))
            if "assembly" in cfg and os.path.isfile(result_contigs_filename):
                message = " * Assembled contigs are in " + support.process_spaces(result_contigs_filename)
                log.info(message)
            if options_storage.rna:
                if "assembly" in cfg and os.path.isfile(result_transcripts_filename):
                    message = " * Assembled transcripts are in " + support.process_spaces(result_transcripts_filename)
                    log.info(message)
                if "assembly" in cfg and os.path.isfile(result_transcripts_paths_filename):
                    message = " * Paths in the assembly graph corresponding to the transcripts are in " + \
                              support.process_spaces(result_transcripts_paths_filename)
                    log.info(message)
            else:
                if "assembly" in cfg and os.path.isfile(result_scaffolds_filename):
                    message = " * Assembled scaffolds are in " + support.process_spaces(result_scaffolds_filename)
                    log.info(message)
                if "assembly" in cfg and os.path.isfile(result_assembly_graph_filename):
                    message = " * Assembly graph is in " + support.process_spaces(result_assembly_graph_filename)
                    log.info(message)
                if "assembly" in cfg and os.path.isfile(result_contigs_paths_filename):
                    message = " * Paths in the assembly graph corresponding to the contigs are in " + \
                              support.process_spaces(result_contigs_paths_filename)
                    log.info(message)
                if "assembly" in cfg and os.path.isfile(result_scaffolds_paths_filename):
                    message = " * Paths in the assembly graph corresponding to the scaffolds are in " + \
                              support.process_spaces(result_scaffolds_paths_filename)
                    log.info(message)
            #log.info("")

        #breaking scaffolds
        if os.path.isfile(result_scaffolds_filename):
            if not os.path.isdir(misc_dir):
                os.makedirs(misc_dir)
            result_broken_scaffolds = os.path.join(misc_dir, "broken_scaffolds.fasta")
            if not os.path.isfile(result_broken_scaffolds) or not options_storage.continue_mode:
                modified, broken_scaffolds = support.break_scaffolds(result_scaffolds_filename,
                    options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)
                if modified:
                    support.write_fasta(result_broken_scaffolds, broken_scaffolds)
                    #log.info(" * Scaffolds broken by " + str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS) +
                    # " Ns are in " + result_broken_scaffolds)

        ### printing WARNINGS SUMMARY
        if not support.log_warnings(log):
            log.info("\n======= SPAdes pipeline finished.")  # otherwise it finished WITH WARNINGS

        if options_storage.test_mode:
            if options_storage.truseq_mode:
                if not os.path.isfile(truseq_long_reads_file):
                    support.error("TEST FAILED: %s does not exist!" % truseq_long_reads_file)
            elif options_storage.rna:
                if not os.path.isfile(result_transcripts_filename):
                    support.error("TEST FAILED: %s does not exist!" % result_transcripts_filename)
            else:
                for result_filename in [result_contigs_filename, result_scaffolds_filename]:
                    if os.path.isfile(result_filename):
                        result_fasta = list(support.read_fasta(result_filename))
                        # correctness check: should be one contig of length 1000 bp
                        correct_number = 1
                        correct_length = 1000
                        if not len(result_fasta):
                            support.error("TEST FAILED: %s does not contain contigs!" % result_filename)
                        elif len(result_fasta) > correct_number:
                            support.error("TEST FAILED: %s contains more than %d contig (%d)!" %
                                          (result_filename, correct_number, len(result_fasta)))
                        elif len(result_fasta[0][1]) != correct_length:
                            if len(result_fasta[0][1]) > correct_length:
                                relation = "more"
                            else:
                                relation = "less"
                            support.error("TEST FAILED: %s contains %s than %d bp (%d bp)!" %
                                          (result_filename, relation, correct_length, len(result_fasta[0][1])))
                    else:
                        support.error("TEST FAILED: " + result_filename + " does not exist!")
            log.info("\n========= TEST PASSED CORRECTLY.")


        log.info("\nSPAdes log can be found here: " + log_filename)
        log.info("")
        log.info("Thank you for using SPAdes!")
        log.removeHandler(log_handler)

    except Exception:
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            if exc_type == OSError and exc_value.errno == errno.ENOEXEC: # Exec format error
                support.error("It looks like you are using SPAdes binaries for another platform.\n" +
                              support.get_spades_binaries_info_message())
            else:
                log.exception(exc_value)
                support.error("exception caught: %s" % exc_type, log)
    except BaseException:  # since python 2.5 system-exiting exceptions (e.g. KeyboardInterrupt) are derived from BaseException
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            log.exception(exc_value)
            support.error("exception caught: %s" % exc_type, log)
def process_spaces(str):
    return support.process_spaces(str)
Example #6
0
def main(args):
    os.environ["LC_ALL"] = "C"

    if len(args) == 1:
        options_storage.usage(spades_version)
        sys.exit(0)

    log = logging.getLogger('spades')
    log.setLevel(logging.DEBUG)

    console = logging.StreamHandler(sys.stdout)
    console.setFormatter(logging.Formatter('%(message)s'))
    console.setLevel(logging.DEBUG)
    log.addHandler(console)

    support.check_binaries(bin_home, log)

    # parse options and safe all parameters to cfg
    cfg, dataset_data = fill_cfg(args, log)

    if options_storage.continue_mode:
        cmd_line, options = get_options_from_params(
            os.path.join(options_storage.output_dir, "params.txt"))
        if not options:
            support.error(
                "failed to parse command line of the previous run! Please restart from the beginning or specify another output directory."
            )
        cfg, dataset_data = fill_cfg(options, log)
        if options_storage.restart_from:
            check_cfg_for_restart_from(cfg)
        options_storage.continue_mode = True

    log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
    if options_storage.continue_mode:
        log_handler = logging.FileHandler(log_filename, mode='a')
    else:
        log_handler = logging.FileHandler(log_filename, mode='w')
    log.addHandler(log_handler)

    if options_storage.continue_mode:
        log.info(
            "\n======= SPAdes pipeline continued. Log can be found here: " +
            log_filename + "\n")
        log.info("Restored from " + cmd_line)
        if options_storage.restart_from:
            updated_params = ""
            flag = False
            for v in args[1:]:
                if v == '-o' or v == '--restart-from':
                    flag = True
                    continue
                if flag:
                    flag = False
                    continue
                updated_params += " " + v
            updated_params = updated_params.strip()
            log.info("with updated parameters: " + updated_params)
            cmd_line += " " + updated_params
        log.info("")

    params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
    params_handler = logging.FileHandler(params_filename, mode='w')
    log.addHandler(params_handler)

    if options_storage.continue_mode:
        log.info(cmd_line)
    else:
        command = "Command line:"
        for v in args:
            command += " " + v
        log.info(command)

    # special case
    if "mismatch_corrector" in cfg and not support.get_lib_ids_by_type(
            dataset_data, 'paired-end'):
        support.warning(
            'cannot perform mismatch correction without at least one paired-end library! Skipping this step.',
            log)
        del cfg["mismatch_corrector"]

    print_used_values(cfg, log)
    log.removeHandler(params_handler)

    if not options_storage.continue_mode:
        log.info("\n======= SPAdes pipeline started. Log can be found here: " +
                 log_filename + "\n")

    # splitting interlaced reads and processing Ns in additional contigs if needed
    if support.dataset_has_interlaced_reads(
            dataset_data) or support.dataset_has_additional_contigs(
                dataset_data):
        dir_for_split_reads = os.path.join(options_storage.output_dir,
                                           'split_input')
        if support.dataset_has_interlaced_reads(dataset_data):
            if not os.path.isdir(dir_for_split_reads):
                os.makedirs(dir_for_split_reads)
            dataset_data = support.split_interlaced_reads(
                dataset_data, dir_for_split_reads, log)
        if support.dataset_has_additional_contigs(dataset_data):
            dataset_data = support.process_Ns_in_additional_contigs(
                dataset_data, dir_for_split_reads, log)
        options_storage.dataset_yaml_filename = os.path.join(
            options_storage.output_dir, "input_dataset.yaml")
        pyyaml.dump(dataset_data,
                    open(options_storage.dataset_yaml_filename, 'w'))
        cfg["dataset"].yaml_filename = options_storage.dataset_yaml_filename

    try:
        # copying configs before all computations (to prevent its changing at run time)
        tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
        if os.path.isdir(
                tmp_configs_dir) and not options_storage.continue_mode:
            shutil.rmtree(tmp_configs_dir)
        if not os.path.isdir(tmp_configs_dir):
            dir_util.copy_tree(os.path.join(spades_home, "configs"),
                               tmp_configs_dir,
                               preserve_times=False)

        corrected_dataset_yaml_filename = ''
        if "error_correction" in cfg:
            STAGE_NAME = "Read error correction"
            bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
            corrected_dataset_yaml_filename = os.path.join(
                bh_cfg.output_dir, "corrected.yaml")
            if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
                and not options_storage.restart_from == "ec":
                log.info("\n===== Skipping %s (already processed). \n" %
                         STAGE_NAME)
            else:
                support.continue_from_here(log)

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in bh_cfg.__dict__:
                    os.environ["HEAPCHECK"] = bh_cfg.heap_check

                if os.path.exists(bh_cfg.output_dir):
                    shutil.rmtree(bh_cfg.output_dir)
                os.makedirs(bh_cfg.output_dir)

                if support.get_lib_ids_by_type(
                        dataset_data, options_storage.LONG_READS_TYPES):
                    not_used_dataset_data = support.get_libs_by_type(
                        dataset_data, options_storage.LONG_READS_TYPES)
                    to_correct_dataset_data = support.rm_libs_by_type(
                        dataset_data, options_storage.LONG_READS_TYPES)
                    to_correct_dataset_yaml_filename = os.path.join(
                        bh_cfg.output_dir, "to_correct.yaml")
                    pyyaml.dump(to_correct_dataset_data,
                                open(to_correct_dataset_yaml_filename, 'w'))
                    bh_cfg.__dict__[
                        "dataset_yaml_filename"] = to_correct_dataset_yaml_filename
                else:
                    not_used_dataset_data = None
                    bh_cfg.__dict__["dataset_yaml_filename"] = cfg[
                        "dataset"].yaml_filename

                log.info("\n===== %s started. \n" % STAGE_NAME)
                hammer_logic.run_hammer(corrected_dataset_yaml_filename,
                                        tmp_configs_dir, bin_home, bh_cfg,
                                        not_used_dataset_data,
                                        ext_python_modules_home, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)

        result_contigs_filename = os.path.join(cfg["common"].output_dir,
                                               "contigs.fasta")
        result_scaffolds_filename = os.path.join(cfg["common"].output_dir,
                                                 "scaffolds.fasta")
        misc_dir = os.path.join(cfg["common"].output_dir, "misc")
        ### if mismatch correction is enabled then result contigs are copied to misc directory
        assembled_contigs_filename = os.path.join(misc_dir,
                                                  "assembled_contigs.fasta")
        assembled_scaffolds_filename = os.path.join(
            misc_dir, "assembled_scaffolds.fasta")
        if "assembly" in cfg:
            STAGE_NAME = "Assembling"
            spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
            spades_cfg.__dict__["result_contigs"] = result_contigs_filename
            spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename

            if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
                                                  or ("mismatch_corrector" in cfg and
                                                      os.path.isfile(assembled_contigs_filename)))\
                and not options_storage.restart_from == 'as' \
                and not (options_storage.restart_from and options_storage.restart_from.startswith('k')):

                log.info("\n===== Skipping %s (already processed). \n" %
                         STAGE_NAME)
                # calculating latest_dir for the next stages
                latest_dir = support.get_latest_dir(
                    os.path.join(spades_cfg.output_dir, "K*"))
                if not latest_dir:
                    support.error(
                        "failed to continue the previous run! Please restart from previous stages or from the beginning.",
                        log)
            else:
                old_result_files = [
                    result_contigs_filename, result_scaffolds_filename,
                    assembled_contigs_filename, assembled_scaffolds_filename
                ]
                for format in [".fasta", ".fastg"]:
                    for old_result_file in old_result_files:
                        if os.path.isfile(old_result_file[:-6] + format):
                            os.remove(old_result_file[:-6] + format)

                if options_storage.restart_from == 'as':
                    support.continue_from_here(log)

                if os.path.isfile(corrected_dataset_yaml_filename):
                    dataset_data = pyyaml.load(
                        open(corrected_dataset_yaml_filename, 'r'))
                    dataset_data = support.relative2abs_paths(
                        dataset_data,
                        os.path.dirname(corrected_dataset_yaml_filename))
                if spades_cfg.disable_rr:
                    spades_cfg.__dict__["rr_enable"] = False
                else:
                    spades_cfg.__dict__["rr_enable"] = True

                if "HEAPCHECK" in os.environ:
                    del os.environ["HEAPCHECK"]
                if "heap_check" in spades_cfg.__dict__:
                    os.environ["HEAPCHECK"] = spades_cfg.heap_check

                log.info("\n===== %s started.\n" % STAGE_NAME)

                # creating dataset
                dataset_filename = os.path.join(spades_cfg.output_dir,
                                                "dataset.info")
                if not os.path.isfile(
                        dataset_filename) or not options_storage.continue_mode:
                    dataset_file = open(dataset_filename, 'w')
                    import process_cfg
                    dataset_file.write(
                        "single_cell" + '\t' +
                        process_cfg.bool_to_str(cfg["dataset"].single_cell) +
                        '\n')
                    if os.path.isfile(corrected_dataset_yaml_filename):
                        dataset_file.write(
                            "reads" + '\t' + process_cfg.process_spaces(
                                corrected_dataset_yaml_filename) + '\n')
                    else:
                        dataset_file.write("reads" + '\t' +
                                           process_cfg.process_spaces(
                                               cfg["dataset"].yaml_filename) +
                                           '\n')
                    if spades_cfg.developer_mode and "reference" in cfg[
                            "dataset"].__dict__:
                        dataset_file.write("reference_genome" + '\t')
                        dataset_file.write(
                            process_cfg.process_spaces(
                                cfg["dataset"].reference) + '\n')
                    dataset_file.close()
                spades_cfg.__dict__["dataset"] = dataset_filename

                latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home,
                                                     spades_cfg, dataset_data,
                                                     ext_python_modules_home,
                                                     log)

                if os.path.isdir(
                        misc_dir) and not options_storage.continue_mode:
                    shutil.rmtree(misc_dir)
                if not os.path.isdir(misc_dir):
                    os.makedirs(misc_dir)

                if options_storage.continue_mode and options_storage.restart_from and options_storage.restart_from.startswith(
                        'k'):
                    k_str = options_storage.restart_from[1:]
                    if k_str.find(":") != -1:
                        k_str = k_str[:k_str.find(":")]
                    support.error(
                        "failed to continue from K=%s because this K was not processed in the original run!"
                        % k_str, log)
                log.info("\n===== %s finished. \n" % STAGE_NAME)

            #corrector
            if "mismatch_corrector" in cfg and (
                    os.path.isfile(result_contigs_filename) or
                (options_storage.continue_mode
                 and os.path.isfile(assembled_contigs_filename))):
                STAGE_NAME = "Mismatch correction"
                to_correct = dict()
                to_correct["contigs"] = (result_contigs_filename,
                                         assembled_contigs_filename)
                if os.path.isfile(result_scaffolds_filename) or (
                        options_storage.continue_mode
                        and os.path.isfile(assembled_scaffolds_filename)):
                    to_correct["scaffolds"] = (result_scaffolds_filename,
                                               assembled_scaffolds_filename)

                # moving assembled contigs (scaffolds) to misc dir
                for assembly_type, (old, new) in to_correct.items():
                    if options_storage.continue_mode and os.path.isfile(new):
                        continue
                    for format in [".fasta", ".fastg"]:
                        if os.path.isfile(old[:-6] + format):
                            shutil.move(old[:-6] + format, new[:-6] + format)

                if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
                    (os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)) \
                    and not options_storage.restart_from == 'mc':
                    log.info("\n===== Skipping %s (already processed). \n" %
                             STAGE_NAME)
                else:
                    if options_storage.restart_from == 'mc':
                        support.continue_from_here(log)

                    log.info("\n===== %s started." % STAGE_NAME)
                    # detecting paired-end library with the largest insert size
                    est_params_data = pyyaml.load(
                        open(os.path.join(latest_dir, "final.lib_data"), 'r'))
                    max_IS_library = None
                    for reads_library in est_params_data:
                        if reads_library['type'] == 'paired-end':
                            if not max_IS_library or float(
                                    reads_library["insert size mean"]) > float(
                                        max_IS_library["insert size mean"]):
                                max_IS_library = reads_library
                    if not max_IS_library:
                        support.error(
                            'Mismatch correction cannot be performed without at least one paired-end library!',
                            log)
                    if not max_IS_library["insert size mean"]:
                        support.warning(
                            'Failed to estimate insert size for all paired-end libraries. Starting Mismatch correction'
                            ' based on the first paired-end library and with default insert size.',
                            log)
                    else:
                        cfg["mismatch_corrector"].__dict__[
                            "insert-size"] = round(
                                max_IS_library["insert size mean"])
                    yaml_dirname = os.path.dirname(
                        options_storage.dataset_yaml_filename)
                    cfg["mismatch_corrector"].__dict__["1"] = list(
                        map(lambda x: os.path.join(yaml_dirname, x),
                            max_IS_library['left reads']))
                    cfg["mismatch_corrector"].__dict__["2"] = list(
                        map(lambda x: os.path.join(yaml_dirname, x),
                            max_IS_library['right reads']))
                    #TODO: add reads orientation

                    import corrector
                    corrector_cfg = cfg["mismatch_corrector"]
                    args = []
                    for key, values in corrector_cfg.__dict__.items():
                        if key == "output-dir":
                            continue

                        # for processing list of reads
                        if not isinstance(values, list):
                            values = [values]
                        for value in values:
                            if len(key) == 1:
                                args.append('-' + key)
                            else:
                                args.append('--' + key)
                            if value is not None:
                                args.append(value)

                    # processing contigs and scaffolds (or only contigs)
                    for assembly_type, (corrected,
                                        assembled) in to_correct.items():
                        if options_storage.continue_mode and os.path.isfile(
                                corrected):
                            log.info("\n== Skipping processing of " +
                                     assembly_type + " (already processed)\n")
                            continue

                        support.continue_from_here(log)
                        log.info("\n== Processing of " + assembly_type + "\n")

                        cur_args = args[:]
                        cur_args += ['-c', assembled]
                        tmp_dir_for_corrector = support.get_tmp_dir(
                            prefix="mis_cor_%s_" % assembly_type)
                        cur_args += ['--output-dir', tmp_dir_for_corrector]

                        # correcting
                        corrector.main(cur_args, ext_python_modules_home, log)

                        result_corrected_filename = os.path.join(
                            tmp_dir_for_corrector, "corrected_contigs.fasta")
                        # moving corrected contigs (scaffolds) to SPAdes output dir
                        if os.path.isfile(result_corrected_filename):
                            shutil.move(result_corrected_filename, corrected)

                        if os.path.isdir(tmp_dir_for_corrector):
                            shutil.rmtree(tmp_dir_for_corrector)

                        assembled_fastg = assembled[:-6] + ".fastg"
                        if os.path.isfile(assembled_fastg):
                            support.create_fastg_from_fasta(
                                corrected, assembled_fastg, log)
                    log.info("\n===== %s finished.\n" % STAGE_NAME)

        if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
            shutil.rmtree(tmp_configs_dir)

        #log.info("")
        if "error_correction" in cfg and os.path.isdir(
                os.path.dirname(corrected_dataset_yaml_filename)):
            log.info(" * Corrected reads are in " + support.process_spaces(
                os.path.dirname(corrected_dataset_yaml_filename) + "/"))
        if "assembly" in cfg and os.path.isfile(result_contigs_filename):
            message = " * Assembled contigs are in " + support.process_spaces(
                result_contigs_filename)
            if os.path.isfile(result_contigs_filename[:-6] + ".fastg"):
                message += " (" + os.path.basename(
                    result_contigs_filename[:-6] + ".fastg") + ")"
            log.info(message)
        if "assembly" in cfg and os.path.isfile(result_scaffolds_filename):
            message = " * Assembled scaffolds are in " + support.process_spaces(
                result_scaffolds_filename)
            if os.path.isfile(result_scaffolds_filename[:-6] + ".fastg"):
                message += " (" + os.path.basename(
                    result_scaffolds_filename[:-6] + ".fastg") + ")"
            log.info(message)
        #log.info("")

        #breaking scaffolds
        if os.path.isfile(result_scaffolds_filename):
            if not os.path.isdir(misc_dir):
                os.makedirs(misc_dir)
            result_broken_scaffolds = os.path.join(misc_dir,
                                                   "broken_scaffolds.fasta")
            if not os.path.isfile(result_broken_scaffolds
                                  ) or not options_storage.continue_mode:
                modified, broken_scaffolds = support.break_scaffolds(
                    result_scaffolds_filename,
                    options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)
                if modified:
                    support.write_fasta(result_broken_scaffolds,
                                        broken_scaffolds)
                    #log.info(" * Scaffolds broken by " + str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS) +
                    # " Ns are in " + result_broken_scaffolds)

        ### printing WARNINGS SUMMARY
        if not support.log_warnings(log):
            log.info("\n======= SPAdes pipeline finished."
                     )  # otherwise it finished WITH WARNINGS

        if options_storage.test_mode:
            for result_filename in [
                    result_contigs_filename, result_scaffolds_filename
            ]:
                if os.path.isfile(result_filename):
                    result_fasta = list(support.read_fasta(result_filename))
                    # correctness check: should be one contig of length 1000 bp
                    correct_number = 1
                    correct_length = 1000
                    if not len(result_fasta):
                        support.error(
                            "TEST FAILED: %s does not contain contigs!" %
                            result_filename)
                    elif len(result_fasta) > correct_number:
                        support.error(
                            "TEST FAILED: %s contains more than %d contig (%d)!"
                            % (result_filename, correct_number,
                               len(result_fasta)))
                    elif len(result_fasta[0][1]) != correct_length:
                        if len(result_fasta[0][1]) > correct_length:
                            relation = "more"
                        else:
                            relation = "less"
                        support.error(
                            "TEST FAILED: %s contains %s than %d bp (%d bp)!" %
                            (result_filename, relation, correct_length,
                             len(result_fasta[0][1])))
                else:
                    support.error("TEST FAILED: " + result_filename +
                                  " does not exist!")
            log.info("\n========= TEST PASSED CORRECTLY.")

        log.info("\nSPAdes log can be found here: " + log_filename)
        log.info("")
        log.info("Thank you for using SPAdes!")
        log.removeHandler(log_handler)

    except Exception:
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            if exc_type == OSError and exc_value.errno == errno.ENOEXEC:  # Exec format error
                support.error(
                    "It looks like you are using SPAdes binaries for another platform.\n"
                    + support.get_spades_binaries_info_message())
            else:
                log.exception(exc_value)
                support.error("exception caught: %s" % exc_type, log)
    except BaseException:  # since python 2.5 system-exiting exceptions (e.g. KeyboardInterrupt) are derived from BaseException
        exc_type, exc_value, _ = sys.exc_info()
        if exc_type == SystemExit:
            sys.exit(exc_value)
        else:
            log.exception(exc_value)
            support.error("exception caught: %s" % exc_type, log)
Example #7
0
def process_spaces(str):
    return support.process_spaces(str)
Example #8
0
 def check_and_report_output_file(output_file_key, message_prefix_text):
     if os.path.isfile(output_files[output_file_key]):
         message = message_prefix_text + support.process_spaces(
             output_files[output_file_key])
         log.info(message)