############################################################################ # Copyright (c) 2015-2017 Saint Petersburg State University # Copyright (c) 2011-2015 Saint Petersburg Academic University # All Rights Reserved # See file LICENSE for details. ############################################################################ import datetime import os import platform import sys from distutils.version import LooseVersion QUAST_HOME = os.path.abspath(os.path.dirname(os.path.dirname(os.path.realpath(__file__)))) PACKAGE_NAME = 'quast_libs' LIBS_LOCATION = os.path.join(QUAST_HOME, PACKAGE_NAME) GIT_ROOT_URL = 'https://raw.githubusercontent.com/ablab/quast/master/' SUPPORTED_PYTHON_VERSIONS = ['2.5+', '3.3+'] # major.minor format only, close ('-') and open ('+') ranges allowed LOGGER_DEFAULT_NAME = 'quast' LOGGER_META_NAME = 'metaquast' # error_log_fpath = os.path.join(LIBS_LOCATION, '..', 'error.log') if platform.system() == 'Darwin': platform_name = 'macosx' else: if platform.architecture()[0] == '64bit': platform_name = 'linux_64' else: platform_name = 'linux_32' # support of large genomes MAX_REFERENCE_LENGTH = 536870908 # Nucmer's max length of a reference file splitted_ref = [] MAX_REFERENCE_FILE_LENGTH = 50000000 # Max length of one part of reference # default values for options contig_thresholds = "0,1000,5000,10000,25000,50000" min_contig = 500 genes_lengths = "0,300,1500,3000" ref_fpath = '' with_gage = False prokaryote = True # former cyclic gene_finding = False ambiguity_usage = 'one' ambiguity_score = 0.99 use_all_alignments = False max_threads = None min_cluster = 65 min_alignment = 0 min_IDY = 95.0 estimated_reference_size = None strict_NA = False scaffolds = False draw_plots = True html_report = True save_json = False metagenemark = False debug = False portable_html = True test = False test_sv = False test_no_ref = False no_check = False no_check_meta = False # for metaQUAST, without checking min-contig unique_mapping = False # for metaQUAST only no_gc = False no_sv = False no_gzip = False show_snps = True glimmer = False is_combined_ref = False check_for_fragmented_ref = False unaligned_part_size = 500 all_labels_from_dirs = False force_nucmer = False # print in stdout only main information silent = False # the following 2 are for web-quast: error_log_fpath = None save_error = False test_output_dirname = "quast_test_output" default_results_root_dirname = "quast_results" output_dirname = "results_" + datetime.datetime.now().strftime('%Y_%m_%d_%H_%M_%S') make_latest_symlink = True default_json_dirname = "json" # names of reports, log, etc. corrected_dirname = "quast_corrected_input" plots_fname = "report.pdf" report_prefix = "report" transposed_report_prefix = "transposed_report" gage_report_prefix = "gage_" html_aux_dir = "report_html_aux" contig_report_fname_pattern = 'contigs_report_%s' icarus_report_fname_pattern = 'all_alignments_%s.tsv' nucmer_output_dirname = 'nucmer_output' # for MetaQUAST downloaded_dirname = "quast_downloaded_references" per_ref_dirname = "runs_per_reference" meta_summary_dir = "summary" not_aligned_name = "not_aligned" combined_output_name = "combined_reference" krona_dirname = "krona_charts" combined_ref_name = 'combined_reference.fasta' downloaded_ref_min_aligned_rate = 0.1 unique_contigs_fname_pattern = 'unique_contigs_%s.tsv' calculate_read_support = False use_input_ref_order = False # for reads analyzer variation_dirname = 'structural_variations' trivial_deletions_fname = 'trivial_deletions.bed' manta_sv_fname = 'manta_sv.bed' used_colors = None used_ls = None # for Icarus draw_svg = False create_icarus_html = True icarus_css_name = 'icarus.css' icarus_script_name = 'build_icarus.js' icarus_dirname = 'icarus_viewers' icarus_html_fname = 'icarus.html' icarus_menu_template_fname = 'icarus_menu_templ.html' icarus_viewers_template_fname = 'viewers_template.html' icarus_link = 'View in Icarus contig browser' contig_size_viewer_fname = 'contig_size_viewer.html' contig_size_viewer_name = 'Contig size viewer' contig_alignment_viewer_name = 'Contig alignment viewer' one_alignment_viewer_name = 'alignment_viewer' alignment_viewer_part_name = 'alignment_viewer_part_' alignment_viewer_fpath = 'alignment_viewer.html' MAX_SIZE_FOR_COMB_PLOT = 50000000 max_contigs_num_for_size_viewer = 1000 min_contig_for_size_viewer = 10000 contig_len_delta = 0.05 min_similar_contig_size = 10000 cov_fpath = None phys_cov_fpath = None # other settings (mostly constants). Can't be changed by command-line options # indels and misassemblies SHORT_INDEL_THRESHOLD = 5 # for separating short and long indels MAX_INDEL_LENGTH = 85 # for separating indels and local misassemblies (Nucmer default value) extensive_misassembly_threshold = 1000 # for separating local and extensive misassemblies (relocation) fragmented_max_indent = MAX_INDEL_LENGTH # for fake translocation in fragmented reference BSS_MAX_SETS_NUMBER = 10 gap_filled_ns_threshold = 0.95 # for parallelization DEFAULT_MAX_THREADS = 4 # this value is used if QUAST fails to determine number of CPUs assemblies_num = 1 memory_efficient = False space_efficient = False # genome analyzer min_gap_size = 50 # for calculating number or gaps in genome coverage min_gene_overlap = 100 # to partial genes/operons finding # basic_stats GC_bin_size = 1.0 GC_contig_bin_size = 5 # plotter and reporting and maybe other modules in the future assembly_labels_by_fpath = {} assemblies_fpaths = [] potential_scaffolds_assemblies = [] max_points = 1500 # max points on plots (== max number of contigs) min_difference = 0 max_coverage_bins = 50 pcnt_covered_for_histogram = 0.9 # for scaffolds dict_of_broken_scaffolds = {} Ns_break_threshold = 10 scaffolds_gap_threshold = 10000 # for searching references in NCBI custom_blast_db_fpath = None downloaded_refs = False identity_threshold = 80 # min % identity min_length = 300 min_bitscore = 300 max_references = 50 # plot extension plot_extension = "pdf" supported_plot_extensions = ['emf', 'eps', 'pdf', 'png', 'ps', 'raw', 'rgba', 'svg', 'svgz'] ### output_dirpath = None reference = None genes = None operons = None labels = None sam = None bam = None bed = None forward_reads = None reverse_reads = None references_txt = None json_output_dirpath = None def check_python_version(): def __next_version(version): components = version.split('.') for i in reversed(range(len(components))): if components[i].isdigit(): components[i] = str(int(components[i]) + 1) break return '.'.join(components) current_version = sys.version.split()[0] supported_versions_msg = [] for supported_versions in SUPPORTED_PYTHON_VERSIONS: major = supported_versions[0] if '-' in supported_versions: # range min_inc, max_inc = supported_versions.split('-') elif supported_versions.endswith('+'): # half open range min_inc, max_inc = supported_versions[:-1], major else: # exact version min_inc = max_inc = supported_versions max_exc = __next_version(max_inc) supported_versions_msg.append("Python%s: %s" % (major, supported_versions.replace('+', " and higher"))) if LooseVersion(min_inc) <= LooseVersion(current_version) < LooseVersion(max_exc): return True sys.stderr.write("ERROR! Python version " + current_version + " is not supported!\n" + "Supported versions are " + ", ".join(supported_versions_msg) + "\n") sys.exit(1) def set_max_threads(logger): global max_threads if max_threads is None: try: import multiprocessing max_threads = max(1, multiprocessing.cpu_count() // 4) except (ImportError, NotImplementedError): logger.warning('Failed to determine the number of CPUs') max_threads = DEFAULT_MAX_THREADS logger.notice('Maximum number of threads is set to ' + str(max_threads) + ' (use --threads option to set it manually)') def quast_version(): revision = None try: from quast_libs import version vers = version.__version__ revision = version.__git_revision__ except ImportError: version_file = open(os.path.join(QUAST_HOME, 'VERSION.txt')) lines = version_file.read().strip().split('\n') version_file.close() vers = lines[0] if len(lines) > 1: revision = lines[1] if revision: return vers + ', ' + revision else: return vers # version = None # build = None # if os.path.isfile(version_fpath): # version_file = open(version_fpath) # version = version_file.readline() # if version: # version = version.strip() # else: # version = "unknown" # build = version_file.readline() # if build: # build = build.strip().lower() # if build: # return version + ", " + build # else: # return version def print_version(meta=False): full_version = 'QUAST v' + quast_version() if meta: full_version += ' (MetaQUAST mode)' sys.stdout.write(full_version + '\n') sys.stdout.flush() def usage(show_hidden=False, meta=False, short=True, stream=sys.stdout): stream.write("") if meta: stream.write('MetaQUAST: QUality ASsessment Tool for Metagenome Assemblies\n') else: stream.write('QUAST: QUality ASsessment Tool for Genome Assemblies\n') stream.write("Version: " + quast_version() + '\n') stream.write("\n") stream.write('Usage: python ' + sys.argv[0] + ' [options] \n') stream.write("\n") stream.write("Options:\n") stream.write("-o --output-dir Directory to store all result files [default: quast_results/results_]\n") if meta: stream.write("-R Comma-separated list of reference genomes or directory with reference genomes\n") stream.write("--references-list Text file with list of reference genomes for downloading from NCBI\n") stream.write("-G --genes File with gene coordinates in the references (GFF, BED, NCBI or TXT)\n") else: stream.write("-R Reference genome file\n") stream.write("-G --genes File with gene coordinates in the reference (GFF, BED, NCBI or TXT)\n") if not short: stream.write("-O --operons File with operon coordinates in the reference (GFF, BED, NCBI or TXT)\n") stream.write("-m --min-contig Lower threshold for contig length [default: %s]\n" % min_contig) stream.write("-t --threads Maximum number of threads [default: 25% of CPUs]\n") stream.write("\n") if short: stream.write("These are basic options. To see the full list, use --help\n") else: stream.write("Advanced options:\n") stream.write("-s --scaffolds Assemblies are scaffolds, split them and add contigs to the comparison\n") stream.write("-l --labels \"label, label, ...\" Names of assemblies to use in reports, comma-separated. If contain spaces, use quotes\n") stream.write("-L Take assembly names from their parent directory names\n") stream.write("-e --eukaryote Genome is eukaryotic\n") if meta: stream.write("-f --gene-finding Predict genes using MetaGeneMark\n") else: stream.write("-f --gene-finding Predict genes using GeneMarkS (prokaryotes, default) or GeneMark-ES (eukaryotes, use --eukaryote)\n") stream.write(" --glimmer Use GlimmerHMM for gene prediction (instead of the default finder, see above)\n") if not meta: stream.write(" --mgm Use MetaGeneMark for gene prediction (instead of the default finder, see above)\n") stream.write(" --gene-thresholds Comma-separated list of threshold lengths of genes to search with Gene Finding module\n") stream.write(" [default: %s]\n" % genes_lengths) if not meta: stream.write(" --est-ref-size Estimated reference size (for computing NGx metrics without a reference)\n") else: stream.write(" --max-ref-number Maximum number of references (per each assembly) to download after looking in SILVA database\n") stream.write(" Set 0 for not looking in SILVA at all [default: %s]\n" % max_references) stream.write(" --blast-db Custom BLAST database (.nsq file). By default, MetaQUAST searches references in SILVA database\n") stream.write(" --use-input-ref-order Use provided order of references in MetaQUAST summary plots (default order: by the best average value).\n") stream.write(" --gage Use GAGE (results are in gage_report.txt)\n") stream.write(" --contig-thresholds Comma-separated list of contig length thresholds [default: %s]\n" % contig_thresholds) stream.write("-u --use-all-alignments Compute genome fraction, # genes, # operons in QUAST v1.* style.\n") stream.write(" By default, QUAST filters Nucmer\'s alignments to keep only best ones\n") stream.write("-i --min-alignment Nucmer's parameter: the minimum alignment length [default: %s]\n" % min_alignment) stream.write(" --min-identity Nucmer's parameter: the minimum alignment identity (80.0, 100.0) [default: %.1f]\n" % min_IDY) stream.write("-a --ambiguity-usage Use none, one, or all alignments of a contig when all of them\n") stream.write(" are almost equally good (see --ambiguity-score) [default: %s]\n" % ambiguity_usage) stream.write(" --ambiguity-score Score S for defining equally good alignments of a single contig. All alignments are sorted \n") stream.write(" by decreasing LEN * IDY% value. All alignments with LEN * IDY% < S * best(LEN * IDY%) are \n") stream.write(" discarded. S should be between 0.8 and 1.0 [default: %.2f]\n" % ambiguity_score) if meta: stream.write(" --unique-mapping Disable --ambiguity-usage=all for the combined reference run,\n") stream.write(" i.e. use user-specified or default ('%s') value of --ambiguity-usage\n" % ambiguity_usage) stream.write(" --strict-NA Break contigs in any misassembly event when compute NAx and NGAx\n") stream.write(" By default, QUAST breaks contigs only by extensive misassemblies (not local ones)\n") stream.write("-x --extensive-mis-size Lower threshold for extensive misassembly size. All relocations with inconsistency\n") stream.write(" less than extensive-mis-size are counted as local misassemblies [default: %s]\n" % extensive_misassembly_threshold) stream.write(" --scaffold-gap-max-size Max allowed scaffold gap length difference. All relocations with inconsistency\n") stream.write(" less than scaffold-gap-size are counted as scaffold gap misassemblies [default: %s]\n" % scaffolds_gap_threshold) stream.write(" --unaligned-part-size Lower threshold for detecting partially unaligned contigs. Such contig should have\n") stream.write(" at least one unaligned fragment >= the threshold [default: %s]\n" % unaligned_part_size) stream.write(" --fragmented Reference genome may be fragmented into small pieces (e.g. scaffolded reference) \n") stream.write(" --fragmented-max-indent Mark translocation as fake if both alignments are located no further than N bases \n") stream.write(" from the ends of the reference fragments [default: %s]\n" % MAX_INDEL_LENGTH) stream.write(" Requires --fragmented option.\n") stream.write(" --plots-format Save plots in specified format [default: %s]\n" % plot_extension) stream.write(" Supported formats: %s\n" % ', '.join(supported_plot_extensions)) stream.write(" --memory-efficient Run Nucmer using one thread, separately per each assembly and each chromosome\n") stream.write(" This may significantly reduce memory consumption on large genomes\n") stream.write(" --space-efficient Create only reports and plots files. .stdout, .stderr, .coords and other aux files will not be created\n") stream.write(" This may significantly reduce space consumption on large genomes. Icarus viewers also will not be built\n") stream.write("-1 --reads1 File with forward reads (in FASTQ format, may be gzipped)\n") stream.write("-2 --reads2 File with reverse reads (in FASTQ format, may be gzipped)\n") stream.write(" --sam SAM alignment file\n") stream.write(" --bam BAM alignment file\n") stream.write(" Reads (or SAM/BAM file) are used for structural variation detection and\n") stream.write(" coverage histogram building in Icarus\n") stream.write(" --sv-bedpe File with structural variations (in BEDPE format)\n") stream.write("\n") stream.write("Speedup options:\n") stream.write(" --no-check Do not check and correct input fasta files. Use at your own risk (see manual)\n") stream.write(" --no-plots Do not draw plots\n") stream.write(" --no-html Do not build html reports and Icarus viewers\n") stream.write(" --no-icarus Do not build Icarus viewers\n") stream.write(" --no-snps Do not report SNPs (may significantly reduce memory consumption on large genomes)\n") stream.write(" --no-gc Do not compute GC% and GC-distribution\n") stream.write(" --no-sv Do not run structural variation detection (make sense only if reads are specified)\n") stream.write(" --no-gzip Do not compress large output files\n") stream.write(" --fast A combination of all speedup options except --no-check\n") if show_hidden: stream.write("\n") stream.write("Hidden options:\n") stream.write("-d --debug Run in a debug mode\n") stream.write("--no-portable-html Do not embed CSS and JS files in HTML report\n") stream.write("-c --min-cluster Nucmer's parameter: the minimum length of a cluster of matches [default: %s]\n" % min_cluster) stream.write("-j --save-json Save the output also in the JSON format\n") stream.write("-J --save-json-to Save the JSON output to a particular path\n") if meta: stream.write("--read-support Use read coverage specified in contig names (SPAdes/Velvet style) for calculating Avg contig read support\n") stream.write("--cov File with read coverage (for Icarus alignment viewer)\n") stream.write("--phys-cov File with physical coverage (for Icarus alignment viewer)\n") stream.write("--no-icarus Do not create Icarus files\n") stream.write("--svg Draw contig alignment plot (in SVG format)\n") stream.write("--force-nucmer Use nucmer instead of E-MEM for aligning contigs. \n") stream.write("\n") stream.write("Other:\n") stream.write(" --silent Do not print detailed information about each step to stdout (log file is not affected)\n") if meta: stream.write(" --test Run MetaQUAST on the data from the test_data folder, output to quast_test_output\n") stream.write(" --test-no-ref Run MetaQUAST without references on the data from the test_data folder, output to quast_test_output\n") stream.write(" MetaQUAST will download SILVA 16S rRNA database (~170 Mb) for searching reference genomes\n") stream.write(" Internet connection is required\n") else: stream.write(" --test Run QUAST on the data from the test_data folder, output to quast_test_output\n") stream.write(" --test-sv Run QUAST with structural variants detection on the data from the test_data folder,\n") stream.write(" output to quast_test_output\n") stream.write("-h --help Print full usage message\n") stream.write("-v --version Print version\n") if show_hidden: stream.write(" --help-hidden Print this usage message with all hidden options\n") stream.write("\n") stream.write("Online QUAST manual is available at http://quast.sf.net/manual\n") stream.flush()