comparison customizemetadata.py @ 2:d122106c317f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd

1:324c12894d59

import argparse
import bz2
import json
import pickle
import re
from pathlib import Path


def load_from_json(json_fp):
    '''
    Read JSON file with marker metadata

    out_metadata = {
        'markers': in_metadata['markers'],
        'taxonomy': in_metadata['taxonomy'],
        'merged_taxon': {}
    }
    # transform merged_taxons tuple keys to string
    for k in in_metadata['merged_taxon']:
        n = ' , '.join(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    # dump metadata to JSON file
    dump_to_json(out_metadata, json_fp)


def transform_json_to_pkl(json_fp, pkl_fp):
    '''
    Read JSON file and drop it to a Pickle file

    out_metadata = {
        'markers': in_metadata['markers'],
        'taxonomy': in_metadata['taxonomy'],
        'merged_taxon': {}
    }
    # transform merged_taxons keys to tuple
    for k in in_metadata['merged_taxon']:
        n = ' , '.split(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    keep_markers_parser.add_argument('--out_json', help="Path to output JSON file")

    args = parser.parse_args()

    if args.function == 'transform_pkl_to_json':
        transform_pkl_to_json(Path(args.pkl), Path(args.json))
    elif args.function == 'transform_json_to_pkl':
        transform_json_to_pkl(Path(args.json), Path(args.pkl))
    elif args.function == 'add_marker':
        add_marker(
            args.in_json,
            args.out_json,

2:d122106c317f

import argparse
import bz2
import json
import pickle
import re
import sys
from importlib.metadata import version
from pathlib import Path

from packaging.version import Version


def load_from_json(json_fp):
    '''
    Read JSON file with marker metadata

    out_metadata = {
        'markers': in_metadata['markers'],
        'taxonomy': in_metadata['taxonomy'],
        'merged_taxon': {}
    }

    # transform merged_taxons tuple keys to string
    for k in in_metadata['merged_taxon']:
        n = ' , '.join(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    # dump metadata to JSON file
    dump_to_json(out_metadata, json_fp)


def validate_map_version(infile, file_type):
    '''
    Check conformity of a user-provided pkl file to Metaphlan SGB (>= v4.0).

    :param infile: Path to input Pickle/JSON file
    :param file_type: String definining file type, pkl or JSON. Case-insensitive
    '''
    file_type = file_type.lower()
    if file_type == 'pkl' or file_type == 'pickle':
        # load metadata from Pickle file
        with bz2.BZ2File(infile, 'r') as pkl_f:
            in_metadata = pickle.load(pkl_f)
    elif file_type == 'json':
        in_metadata = load_from_json(infile)
    else:
        raise ValueError("Unsupported file type to validate.")

    # Get metaphlan version in $PATH
    metaphlan_version = Version(version('metaphlan'))

    # Ensure that there are 8 taxonomy levels separated with "|"s.
    # v3 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276', 4404432)
    # v4 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276|', 4404432)
    for k in in_metadata['taxonomy']:
        if (in_metadata['taxonomy'][k][0].count('|') != 7 and metaphlan_version >= Version('4')) or (in_metadata['taxonomy'][k][0].count('|') != 6 and metaphlan_version < Version('4')):
            # raise ValueError("Missing/Extra values in GCA list")
            print("The input taxonomy mapping file %s is incompatible with Metaphlan v.%s in $PATH." % (infile, metaphlan_version))
            sys.exit(42)

    print("%s is compatible with Metaphlan v.%s." % (infile, metaphlan_version))


def transform_json_to_pkl(json_fp, pkl_fp):
    '''
    Read JSON file and drop it to a Pickle file

    out_metadata = {
        'markers': in_metadata['markers'],
        'taxonomy': in_metadata['taxonomy'],
        'merged_taxon': {}
    }

    # transform merged_taxons keys to tuple
    for k in in_metadata['merged_taxon']:
        n = ' , '.split(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    keep_markers_parser.add_argument('--out_json', help="Path to output JSON file")

    args = parser.parse_args()

    if args.function == 'transform_pkl_to_json':
        validate_map_version(Path(args.pkl), 'pkl')
        transform_pkl_to_json(Path(args.pkl), Path(args.json))
    elif args.function == 'transform_json_to_pkl':
        validate_map_version(Path(args.json), 'json')
        transform_json_to_pkl(Path(args.json), Path(args.pkl))
    elif args.function == 'add_marker':
        add_marker(
            args.in_json,
            args.out_json,