command.py

#!/usr/bin/env python3
from . import _program
from pangolin import __version__
from pangolin.utils import data_checks
try:
    import pangolin_data
except:
    data_checks.install_error("pangolin_data", "https://github.com/cov-lineages/pangolin-data.git")

try:
    import scorpio
except:
    data_checks.install_error("scorpio", "https://github.com/cov-lineages/scorpio.git")

try:
    import constellations
except:
    data_checks.install_error("constellations", "https://github.com/cov-lineages/constellations.git")

import os
import sys
import argparse

try:
    import snakemake
except:
    sys.stderr.write(cyan(f'Error: package `{snakemake}` not found, please install snakemake or update pangolin environment.\n'))
    sys.exit(-1)


from pangolin.utils.log_colours import green,cyan
from pangolin.utils import dependency_checks

from pangolin.utils import update


from pangolin.utils.config import *
from pangolin.utils.initialising import *
import pangolin.utils.io_parsing as io

from pangolin.utils.report_collation import generate_final_report,get_voc_list

thisdir = os.path.abspath(os.path.dirname(__file__))
cwd = os.getcwd()


def main(sysargs = sys.argv[1:]):
    parser = argparse.ArgumentParser(prog = _program,
    description='pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages',
    usage='''pangolin <query> [options]''')

    io_group = parser.add_argument_group('Input-Output options')
    io_group.add_argument('query', nargs="*", help='Query fasta file of sequences to analyse.')
    io_group.add_argument('-o','--outdir', action="store",help="Output directory. Default: current working directory")
    io_group.add_argument('--outfile', action="store",help="Optional output file name. Default: lineage_report.csv")
    io_group.add_argument('--tempdir',action="store",help="Specify where you want the temp stuff to go. Default: $TMPDIR")
    io_group.add_argument("--no-temp",action="store_true",help="Output all intermediate files, for dev purposes.")
    io_group.add_argument('--alignment', action="store_true",help="Output multiple sequence alignment.")
    io_group.add_argument('--alignment-file', action="store",help="Multiple sequence alignment file name.")
    io_group.add_argument('--expanded-lineage', action="store_true", default=False, help="Optional expanded lineage from alias.json in report.")


    a_group = parser.add_argument_group('Analysis options')
    a_group.add_argument('--analysis-mode', action="store",help="""Pangolin includes multiple analysis engines: UShER and pangoLEARN.
Scorpio is used in conjunction with UShER/ pangoLEARN to curate variant of concern (VOC)-related lineage calls.
UShER is the default and is selected using option "usher" or "accurate".
pangoLEARN can alternatively be selected using "pangolearn" or "fast".
Finally, it is possible to skip the UShER/ pangoLEARN step by selecting "scorpio" mode, but in this case only VOC-related lineages will be assigned. 
""")
    
    a_group.add_argument("--skip-designation-cache", action='store_true', default=False, help="Developer option - do not use designation cache to assign lineages.",dest="skip_designation_cache")
    a_group.add_argument("--skip-scorpio", action='store_true', default=False, help="Developer option - do not use scorpio to check VOC/VUI lineage assignments.",dest="skip_scorpio")

    a_group.add_argument('--max-ambig', action="store", default=0.3, type=float,help="Maximum proportion of Ns allowed for pangolin to attempt assignment. Default: 0.3",dest="maxambig")
    a_group.add_argument('--min-length', action="store", default=25000, type=int,help="Minimum query length allowed for pangolin to attempt assignment. Default: 25000",dest="minlen")
    a_group.add_argument('--usher', action='store_true', default=False, help=argparse.SUPPRESS)

    d_group = parser.add_argument_group('Data options')
    d_group.add_argument("--update", action='store_true', default=False, help="Automatically updates to latest release of pangolin, pangolin-data, scorpio and constellations (and pangolin-assignment if it has been installed using --add-assignment-cache), then exits.")
    d_group.add_argument("--update-data", action='store_true',dest="update_data", default=False, help="Automatically updates to latest release of constellations and pangolin-data, including the pangoLEARN model, UShER tree file and alias file (also pangolin-assignment if it has been installed using --add-assignment-cache), then exits.")
    d_group.add_argument('--add-assignment-cache', action='store_true', dest="add_assignment_cache", default=False, help="Install the pangolin-assignment repository for use with --use-assignment-cache.  This makes updates slower and makes pangolin slower for small numbers of input sequences but much faster for large numbers of input sequences.")
    d_group.add_argument('--use-assignment-cache', action='store_true', dest="use_assignment_cache", default=False, help="Use assignment cache from optional pangolin-assignment repository. NOTE: the repository must be installed by --add-assignment-cache before using --use-assignment-cache.")
    d_group.add_argument('-d', '--datadir', action='store',dest="datadir",help="Data directory minimally containing the pangoLEARN model, header files and UShER tree. Default: Installed pangolin-data package.")
    d_group.add_argument('--usher-tree', action='store', dest='usher_protobuf', help="UShER Mutation Annotated Tree protobuf file to use instead of default from pangolin-data repository or --datadir.")
    d_group.add_argument('--assignment-cache', action='store', dest='assignment_cache', help="Cached precomputed assignment file to use instead of default from pangolin-assignment repository.  Does not require installation of pangolin-assignment.")

    m_group = parser.add_argument_group('Misc options')
    m_group.add_argument("--aliases", action='store_true', default=False, help="Print Pango alias_key.json and exit.")
    m_group.add_argument("-v","--version", action='version', version=f"pangolin {__version__}")
    m_group.add_argument("-pv","--pangolin-data-version", action='version', version=f"pangolin-data {pangolin_data.__version__}",help="show version number of pangolin data files (UShER tree and pangoLEARN model files) and exit.")
    m_group.add_argument("--all-versions", action='store_true',dest="all_versions", default=False, help="Print all tool, dependency, and data versions then exit.")
    m_group.add_argument("--verbose",action="store_true",help="Print lots of stuff to screen")
    m_group.add_argument("-t","--threads",action="store",default=1,type=int, help="Number of threads")


    if len(sysargs)<1:
        parser.print_help()
        sys.exit(-1)
    else:
        args = parser.parse_args(sysargs)

    # Initialise config dict
    config = setup_config_dict(cwd)
    data_checks.check_install(config)
    set_up_verbosity(config)

    if args.usher:
        sys.stderr.write(cyan(f"--usher is a pangolin v3 option and is deprecated in pangolin v4.  UShER is now the default analysis mode.  Use --analysis-mode to explicitly set mode.\n"))

    setup_data(args.datadir,config[KEY_ANALYSIS_MODE], config)

    if args.add_assignment_cache:
        update.install_pangolin_assignment()

    if args.update:
        version_dictionary = {'pangolin': __version__,
                              'pangolin-data': config[KEY_PANGOLIN_DATA_VERSION],
                              'constellations': config[KEY_CONSTELLATIONS_VERSION],
                              'scorpio': config[KEY_SCORPIO_VERSION]}
        update.add_pangolin_assignment_if_installed(version_dictionary)
        update.update(version_dictionary)

    if args.update_data:
        version_dictionary = {'pangolin-data': config[KEY_PANGOLIN_DATA_VERSION],
                              'constellations': config[KEY_CONSTELLATIONS_VERSION]}
        update.add_pangolin_assignment_if_installed(version_dictionary)
        update.update(version_dictionary, args.datadir)

    # install_pangolin_assignment doesn't exit so that --update/--update-data can be given at the
    # same time (or a query file).  If --add-assignment-cache is the only arg, exit without error.
    if args.add_assignment_cache and not args.query:
        sys.exit(0)

    # add flag to config for whether to run scorpio
    if args.skip_scorpio:
        print(green(f"****\nPangolin skipping scorpio steps.\n****"))
        config[KEY_SKIP_SCORPIO] = True
    
    if args.expanded_lineage:
        print(green(f"****\nAdding expanded lineage column to output.\n****"))
        config[KEY_EXPANDED_LINEAGE] = True
        
    # Parsing analysis mode flags to return one of 'usher' or 'pangolearn'
    config[KEY_ANALYSIS_MODE] = set_up_analysis_mode(args.analysis_mode, config[KEY_ANALYSIS_MODE])
    print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****"))
    if config[KEY_ANALYSIS_MODE] == "scorpio":
        print(cyan(f"Warning: in `scorpio` mode only variants of concern (VOCs) defined in constellations can be assigned. `Version` column corresponds to constellation_version.\n"))

    snakefile = get_snakefile(thisdir,config[KEY_ANALYSIS_MODE])

    config[KEY_DESIGNATION_CACHE],config[KEY_ALIAS_FILE] = data_checks.find_designation_cache_and_alias(config[KEY_DATADIR],DESIGNATION_CACHE_FILE,ALIAS_FILE)
    if args.aliases:
        print_alias_file_exit(config[KEY_ALIAS_FILE])

    if args.all_versions:
        print_versions_exit(config)

    # to enable not having to pass a query if running update
    # by allowing query to accept 0 to many arguments
    
    print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****"))
    print_ram_warning(config[KEY_ANALYSIS_MODE])

#   setup outdir and outfiles
    config[KEY_OUTDIR] = io.set_up_outdir(args.outdir,cwd,config[KEY_OUTDIR])
    config[KEY_OUTFILE] = io.set_up_outfile(args.outfile, config[KEY_OUTFILE],config[KEY_OUTDIR])
    io.set_up_tempdir(args.tempdir,args.no_temp,cwd,config[KEY_OUTDIR], config)
    config[KEY_ALIGNMENT_FILE],config[KEY_ALIGNMENT_OUT] = io.parse_alignment_options(args.alignment, config[KEY_OUTDIR], config[KEY_TEMPDIR],args.alignment_file, config[KEY_ALIGNMENT_FILE])
    parse_qc_thresholds(args.maxambig, args.minlen, config[KEY_REFERENCE_FASTA], config)
    config[KEY_QUERY_FASTA] = io.find_query_file(cwd, config[KEY_TEMPDIR], args.query)

    io.quick_check_query_file(cwd, args.query, config[KEY_QUERY_FASTA])

    if config[KEY_ANALYSIS_MODE] == "usher":
        # Find usher protobuf file (and if specified, assignment cache file too)
        data_checks.get_datafiles(config[KEY_DATADIR],usher_files,config)
        if args.usher_protobuf:
            config[KEY_USHER_PB] = data_checks.check_file_arg(args.usher_protobuf, cwd, '--usher-tree')
            print(green(f"Using usher tree file {args.usher_protobuf}"))
        if args.assignment_cache:
            config[KEY_ASSIGNMENT_CACHE] = data_checks.check_file_arg(args.assignment_cache, cwd, '--assignment-cache')
            print(green(f"Using assignment cache file {args.assignment_cache}"))
        elif args.use_assignment_cache:
            config[KEY_ASSIGNMENT_CACHE] = data_checks.get_assignment_cache(USHER_ASSIGNMENT_CACHE_FILE, config)
            print(green("Using pangolin-assignment cache"))
        else:
            config[KEY_ASSIGNMENT_CACHE] = ""

    elif config[KEY_ANALYSIS_MODE] == "pangolearn":
        # find designation cache and the model files
        data_checks.get_datafiles(config[KEY_DATADIR],pangolearn_files,config)
        if args.use_assignment_cache or args.assignment_cache:
            sys.stderr.write(cyan(f"Warning: --use-assignment-cache and --assignment-cache are ignored when --analysis-mode is 'fast' or 'pangolearn'.\n"))
    
    preprocessing_snakefile = get_snakefile(thisdir,"preprocessing")

    if args.verbose:
        print(green("\n**** CONFIG ****"))
        for k in sorted(config):
            print(green(k), config[k])

        status = snakemake.snakemake(preprocessing_snakefile, printshellcmds=True, forceall=True, force_incomplete=True,
                                        workdir=config[KEY_TEMPDIR],config=config, cores=args.threads,lock=False
                                        )
    else:
        logger = custom_logger.Logger()
        status = snakemake.snakemake(preprocessing_snakefile, printshellcmds=False, forceall=True,force_incomplete=True,workdir=config[KEY_TEMPDIR],
                                    config=config, cores=args.threads,lock=False,quiet=True,log_handler=logger.log_handler
                                    )
    if status: 
        if config[KEY_ANALYSIS_MODE] != "scorpio":
            if config[KEY_VERBOSE]:
                print(green("\n**** CONFIG ****"))
                for k in sorted(config):
                    print(green(k), config[k])

                status = snakemake.snakemake(snakefile, printshellcmds=True, forceall=True, force_incomplete=True,
                                                workdir=config[KEY_TEMPDIR],config=config, cores=args.threads,lock=False
                                                )
            else:
                logger = custom_logger.Logger()
                status = snakemake.snakemake(snakefile, printshellcmds=False, forceall=True,force_incomplete=True,workdir=config[KEY_TEMPDIR],
                                            config=config, cores=args.threads,lock=False,quiet=True,log_handler=logger.log_handler
                                            )
        else:
            status = True
       
        if status: 
            
            ## Collate the report here

            preprocessing_csv = os.path.join(config[KEY_TEMPDIR],"preprocessing.csv")
            inference_csv = os.path.join(config[KEY_TEMPDIR],"inference_report.csv")
            cached_csv = os.path.join(config[KEY_TEMPDIR],"cache_assigned.csv")
            constellation_list = get_voc_list(os.path.join(config[KEY_TEMPDIR], "get_constellations.txt"), config[KEY_ALIAS_FILE])

            generate_final_report(preprocessing_csv, inference_csv, cached_csv, config[KEY_ALIAS_FILE], constellation_list, config[KEY_PANGOLIN_DATA_VERSION],config[KEY_ANALYSIS_MODE], args.skip_designation_cache, config[KEY_OUTFILE],config)

            print(green(f"****\nOutput file written to: ") + config[KEY_OUTFILE])

            if config[KEY_ALIGNMENT_OUT]:
                print(green(f"****\nOutput alignment written to: ") + config[KEY_ALIGNMENT_FILE])

            io.cleanup(args.no_temp,config[KEY_TEMPDIR])

            return 0

        io.cleanup(no_temp,tempdir)
        return 1
    io.cleanup(no_temp,tempdir)
    return 1

if __name__ == '__main__':
    main()