comparison data_manager/kraken2_build_database.py @ 6:9002633b4737 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97

5:2f27f3b86827

    def __str__(self):
        return self.value


class StandardPrebuiltSizes(Enum):
    full = 'full'
    gb_16 = '16'
    gb_8 = '8'

    def __str__(self):
        return self.value

    }

    return data_table_entry


def kraken2_build_standard_prebuilt(standard_prebuilt_size, prebuilt_date, target_directory, data_table_name=DATA_TABLE_NAME):

    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")

    database_value = "_".join([
        now,
        "standard_prebuilt",
        standard_prebuilt_size
    ])

    database_name = " ".join([
        "Standard (Prebuilt)",
        standard_prebuilt_size,
        "(Downloaded:",
        now + ")"
    ])

    database_path = database_value

    size_to_url_str = {
        'full': '',
        '16': '_16gb',
        '8': '_8gb',
    }
    # we may need to let the user choose the date when new DBs are posted.
    date_url_str = prebuilt_date.replace('-', '')
    standard_prebuilt_size_url = size_to_url_str[standard_prebuilt_size]
    # download the pre-built database
    try:
        download_url = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard%s_%s.tar.gz' % (standard_prebuilt_size_url, date_url_str)
        src = urlopen(download_url)
    except URLError as e:
        print('url: ' + download_url, file=sys.stderr)
        print(e, file=sys.stderr)
        exit(1)

    parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
    parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
    parser.add_argument('--threads', dest='threads', default=1, help='threads')
    parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
    parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
    parser.add_argument('--standard-prebuilt-size', dest='standard_prebuilt_size', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Size of standard prebuilt database to download (only applies to --database-type standard_prebuilt. Options are: "8", "16", "full".)')
    parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
    parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
    parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
    parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')

            kraken2_args,
            target_directory,
        )
    elif str(args.database_type) == 'standard_prebuilt':
        data_manager_output = kraken2_build_standard_prebuilt(
            str(args.standard_prebuilt_size),
            str(args.prebuilt_date),
            target_directory
        )
    elif str(args.database_type) == 'minikraken':
        data_manager_output = kraken2_build_minikraken(

6:9002633b4737

    def __str__(self):
        return self.value


class StandardPrebuiltSizes(Enum):
    viral = "viral"
    minusb = "minusb"
    standard = "standard"
    standard_08gb = "standard_08gb"
    standard_16gb = "standard_16gb"
    pluspf = "pluspf"
    pluspf_08gb = "pluspf_08gb"
    pluspf_16gb = "pluspf_16gb"
    pluspfp = "pluspfp"
    pluspfp_08gb = "pluspfp_08gb"
    pluspfp_16gb = "pluspfp_16gb"

    def __str__(self):
        return self.value

    }

    return data_table_entry


def kraken2_build_standard_prebuilt(prebuilt_db, prebuilt_date, target_directory, data_table_name=DATA_TABLE_NAME):

    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")

    prebuild_name = {
        'viral': "Viral",
        'minusb': "MinusB (archaea, viral, plasmid, human, UniVec_Core)",
        'standard': "Standard-Full (archaea, bacteria, viral, plasmid, human,UniVec_Core)",
        'standard_08gb': "Standard-8 (Standard with DB capped at 8 GB)",
        'standard_16gb': "Standard-16 (Standard with DB capped at 16 GB)",
        'pluspf': "PlusPF (Standard plus protozoa and fungi)",
        'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
        'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
        'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
        'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
        'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)"
    }

    database_value = "_".join([
        now,
        "standard_prebuilt",
        prebuilt_db,
        prebuilt_date
    ])

    database_name = " ".join([
        "Prebuilt Refseq indexes: ",
        prebuild_name[prebuilt_db],
        "(Version: ",
        prebuilt_date,
        "- Downloaded:",
        now + ")"
    ])

    database_path = database_value

    # we may need to let the user choose the date when new DBs are posted.
    date_url_str = prebuilt_date.replace('-', '')
    # download the pre-built database
    try:
        download_url = 'https://genome-idx.s3.amazonaws.com/kraken/k2_%s_%s.tar.gz' % (prebuilt_db, date_url_str)
        src = urlopen(download_url)
    except URLError as e:
        print('url: ' + download_url, file=sys.stderr)
        print(e, file=sys.stderr)
        exit(1)

    parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
    parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
    parser.add_argument('--threads', dest='threads', default=1, help='threads')
    parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
    parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
    parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt.')
    parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
    parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
    parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
    parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')

            kraken2_args,
            target_directory,
        )
    elif str(args.database_type) == 'standard_prebuilt':
        data_manager_output = kraken2_build_standard_prebuilt(
            str(args.prebuilt_db),
            str(args.prebuilt_date),
            target_directory
        )
    elif str(args.database_type) == 'minikraken':
        data_manager_output = kraken2_build_minikraken(