New upstream version 2.7.6

repo: 092c2fe2278cb7f0b18d81faeb4aab98b89dc096

node: b2f9b3286d4be376805e3b5c26cf141ed375c605

node: cbd7880df400b453b8beb4e62b39e4a23b5523b6

branch: default

tag: 2.7.5

tag: 2.7.6

8963e486f79043c79a299f7a684e4550b0115c32 2.7.0

d8ab9ca4244c09a7a4995042a99fbba1e3598ac0 2.7.1

a1fe0d15320c04f69d56f1b7dd31cff972a7b8df 2.7.2

b2f9b3286d4be376805e3b5c26cf141ed375c605 2.7.5

847b250adbe97b9f4adc7e15f0d4bb5a66e782ec 2.7.4

178d1aaf4ac76e5d5477833e8e614104dcd32088 2.7.3

__author__ = ('Nicola Segata (nicola.segata@unitn.it), '

              'Duy Tin Truong, '

              'Francesco Asnicar (f.asnicar@unitn.it)')

__version__ = '2.7.5'

__date__ = '6 February 2018'

__version__ = '2.7.6'

__date__ = '2 March 2018'

import sys

            "\n------------------------------------------------------------------- \n \n\n"

            "\n========== MetaPhlAn 2 strain tracking ============================ \n\n"

            "\n========== Marker level analysis ============================ \n\n"

            "MetaPhlAn 2 introduces the capability of charachterizing organisms at the strain level using non\n"

            "aggregated marker information. Such capability comes with several slightly different flavours and \n"

            "are a way to perform strain tracking and comparison across multiple samples.\n"

    arg('--mpa_pkl', type=str, default=None,

        help="The metadata pickled MetaPhlAn file [deprecated]")

    arg('--bowtie2db', metavar="METAPHLAN_BOWTIE2_DB", type=str, default=None,

    arg('--bowtie2db', metavar="METAPHLAN_BOWTIE2_DB", type=str, default=DEFAULT_DB_FOLDER,

        help=("The BowTie2 database file of the MetaPhlAn database. Used if "

              "--input_type is fastq, fasta, multifasta, or multifastq "

              "[deprecated]"))

              "--input_type is fastq, fasta, multifasta, or multifastq [default "+DEFAULT_DB_FOLDER+"]\n"))

    arg('-x', '--index', type=str, default='v20_m200',

        help=("Specify the id of the database version to use. If the database "

              "files are not found on the local MetaPhlAn2 installation they "

              "will be automatically downloaded"))

        help=("Specify the id of the database version to use. If the database\n"

              "files are not found on the local MetaPhlAn2 installation they\n"

              "will be automatically downloaded\n"))

    bt2ps = ['sensitive', 'very-sensitive', 'sensitive-local',

             'very-sensitive-local']

    bt2ps = ['sensitive', 'very-sensitive', 'sensitive-local', 'very-sensitive-local']

    arg('--bt2_ps', metavar="BowTie2 presets", default='very-sensitive',

        choices=bt2ps, help="Presets options for BowTie2 (applied only when a "

                            "multifasta file is provided)\n"

            sys.stderr.write("Fatal error running '{}'\nError message: '{}'\n\n".format(' '.join(bt2_cmd), e))

            sys.exit(1)

    sys.stderr.write('Removing uncompress database {}\n'.format(fna_file))

    os.remove(fna_file)

def check_and_install_database(index, bowtie2_build, nproc):

def check_and_install_database(index, bowtie2_db, bowtie2_build, nproc):

    """ Check if the database is installed, if not download and install """

    if len(glob(os.path.join(DEFAULT_DB_FOLDER, "mpa_{}*".format(index)))) >= 7:

    if len(glob(os.path.join(bowtie2_db, "mpa_{}*".format(index)))) >= 7:

        return

    # download the tar archive and decompress

    sys.stderr.write("\nDownloading MetaPhlAn2 database\nPlease note due to "

                     "the size this might take a few minutes\n")

    download_unpack_tar(DATABASE_DOWNLOAD, index, DEFAULT_DB_FOLDER, bowtie2_build, nproc)

    download_unpack_tar(DATABASE_DOWNLOAD, index, bowtie2_db, bowtie2_build, nproc)

    sys.stderr.write("\nDownload complete\n")

def set_mapping_arguments(index):

def set_mapping_arguments(index, bowtie2_db):

    mpa_pkl = 'mpa_pkl'

    bowtie2db = 'bowtie2db'

    if os.path.isfile(os.path.join(DEFAULT_DB_FOLDER, "mpa_{}.pkl".format(index))):

        mpa_pkl = os.path.join(DEFAULT_DB_FOLDER, "mpa_{}.pkl".format(index))

    if os.path.isfile(os.path.join(bowtie2_db, "mpa_{}.pkl".format(index))):

        mpa_pkl = os.path.join(bowtie2_db, "mpa_{}.pkl".format(index))

    if glob(os.path.join(DEFAULT_DB_FOLDER, "mpa_{}*.bt2".format(index))):

        bowtie2db = os.path.join(DEFAULT_DB_FOLDER, "mpa_{}".format(index))

    if glob(os.path.join(bowtie2_db, "mpa_{}*.bt2".format(index))):

        bowtie2db = os.path.join(bowtie2_db, "mpa_{}".format(index))

    return (mpa_pkl, bowtie2db)

    pars = read_params(sys.argv)

    # check if the database is installed, if not then install

    check_and_install_database(pars['index'], pars['bowtie2_build'],

                               pars['nproc'])

    check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'])

    if pars['install']:

        sys.stderr.write('The database is installed\n')

        return

    # set correct map_pkl and bowtie2db variables

    pars['mpa_pkl'], pars['bowtie2db'] = set_mapping_arguments(pars['index'])

    pars['mpa_pkl'], pars['bowtie2db'] = set_mapping_arguments(pars['index'], pars['bowtie2db'])

    #if pars['inp'] is None and ( pars['input_type'] is None or  pars['input_type'] == 'automatic'):

    #    sys.stderr.write( "The --input_type parameter need top be specified when the "

                            for p in ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"]]):

            sys.stderr.write("No MetaPhlAn BowTie2 database found (--index "

                             "option)!\nExpecting location {}\nExiting..."

                             .format(DEFAULT_DB_FOLDER))

                             .format(pars['bowtie2db']))

            sys.exit(1)

        if bow:

import ConfigParser

import dendropy

import numpy

import ipdb

# import ipdb

def read_params():