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Source code for galaxy.tool_util.edam_util

import os
from typing import Dict, Optional, TextIO

    from edam_ontology.streams import tabular_stream
except ImportError:
    tabular_stream = None

EDAM_PREFIX = 'http://edamontology.org/'

ROOT_OPERATION = 'operation_0004'
ROOT_TOPIC = 'topic_0003'

[docs]def load_edam_tree(path: Optional[str] = None): if path is not None: assert os.path.exists(path), f"Failed to load EDAM tabular data at [{path}] path does not exist." handle = open(path) else: assert tabular_stream is not None, "Failed to load optional import from edam-onotology package, install using [pip install edam-ontology]." handle = tabular_stream() return load_edam_tree_from_tsv_stream(handle)
def load_edam_tree_from_tsv_stream(tsv_stream: TextIO): edam: Dict[str, Dict] = {} def _recurse_edam_parents(term, path=None): if edam[term]['parents'] and len(edam[term]['parents']) > 0: for parent in edam[term]['parents']: yield from _recurse_edam_parents(parent, path + [parent]) else: yield path is_first = True for line in tsv_stream.readlines(): fields = line.split('\t') if is_first: columns = {} for i, field in enumerate(fields): columns[field] = i is_first = False defintion_column = columns["http://www.geneontology.org/formats/oboInOwl#hasDefinition"] term_column = columns["Class ID"] label_column = columns["Preferred Label"] parents_column = columns["Parents"] continue term = fields[term_column] if not term.startswith(EDAM_PREFIX): continue term_id = term[len(EDAM_PREFIX):] # Only care about formats and operations if not (term_id.startswith('operation_') or term_id.startswith('topic_')): continue parents = fields[parents_column].split('|') edam[term_id] = { 'label': fields[label_column], 'definition': fields[defintion_column].strip('"'), 'parents': [x[len(EDAM_PREFIX):] for x in parents if x.startswith(EDAM_PREFIX)], } for term in sorted(edam.keys()): tails = [] for x in _recurse_edam_parents(term, path=[]): if x[-2:] not in tails: tails.append(x[-2:]) edam[term]['path'] = tails return edam __all__ = ('load_edam_tree', 'ROOT_OPERATION', 'ROOT_TOPIC')