Biomedical Databases Parsers¶

cancerGenomeInterpreterParser.py¶

parser(databases_directory, download=True)[source]¶

corumParser.py¶

parser(databases_directory, download=True)[source]¶

disgenetParser.py¶

parser(databases_directory, download=True)[source]¶

readDisGeNetProteinMapping(config, directory)[source]¶

readDisGeNetDiseaseMapping(config, directory)[source]¶

drugBankParser.py¶

parser(databases_directory)[source]¶

extract_drugs(config, directory)[source]¶

parseDrugBankVocabulary(config, directory)[source]¶

build_relationships_from_DrugBank(config, drugs)[source]¶

build_drug_entity(config, drugs)[source]¶

build_DrugBank_dictionary(config, directory, drugs)[source]¶

drugGeneInteractionDBParser.py¶

parser(databases_directory, download=True)[source]¶

exposomeParser.py¶

parser(databases_directory, download=True)[source]¶

parseBiomarkersFile(fhandler, file_name)[source]¶

parseCorrelationsFile(fhandler, file_name, biomarkers, mapping)[source]¶

foodbParser.py¶

parser(databases_directory, download=True)[source]¶

parseContents(fhandler)[source]¶

parseFood(fhandler)[source]¶

parseCompounds(fhandler)[source]¶

goaParser.py¶

parser(databases_dir, download=True)[source]¶

parse_annotations_with_pandas(annotation_file, valid_proteins=None)[source]¶

gwasCatalogParser.py¶

parser(databases_directory, download=True)[source]¶

hgncParser.py¶

parser(databases_directory, download=True)[source]¶

hmdbParser.py¶

parser(databases_directory, download=True)[source]¶

extract_metabolites(config, directory, download=True)[source]¶

build_metabolite_entity(config, directory, metabolites)[source]¶

build_relationships_from_HMDB(config, metabolites, mapping)[source]¶

build_HMDB_dictionary(directory, metabolites)[source]¶

hpaParser.py¶

parser(databases_directory, download=True)[source]¶

parsePathologyFile(config, fhandler, file_name, protein_mapping, disease_mapping)[source]¶

intactParser.py¶

parser(databases_directory, download=True)[source]¶

jensenlabParser.py¶

parser(databases_directory, download=True)[source]¶

parsePairs(config, databases_directory, qtype, mapping, download=True)[source]¶

mutationDsParser.py¶

parser(databases_directory, download=True)[source]¶

oncokbParser.py¶

parser(databases_directory, download=True)[source]¶

pathwayCommonsParser.py¶

parser(databases_directory, download=True)[source]¶

pfamParser.py¶

parser(databases_directory, import_directory, download=True, updated_on=None)[source]¶

print_files(data, header, outputfile, is_first, filter_for=None)[source]¶

pspParser.py¶

parser(databases_directory)[source]¶

parseSites(fhandler, modifications)[source]¶

parseKinaseSubstrates(fhandler, modifications)[source]¶

parseRegulationAnnotations(fhandler, modifications, mapping)[source]¶

parseDiseaseAnnotations(fhandler, modifications, mapping)[source]¶

reactomeParser.py¶

parser(databases_directory, download=True)[source]¶

parsePathways(config, databases_directory, fhandler)[source]¶

parsePathwayHierarchy(fhandler)[source]¶

parsePathwayRelationships(config, fhandler, mapping=None)[source]¶

refseqParser.py¶

parser(databases_directory, download=True)[source]¶

siderParser.py¶

parser(databases_directory, drug_source, download=True)[source]¶

parserIndications(databases_directory, drugMapping, phenotypeMapping, download=True)[source]¶

signorParser.py¶

parser(databases_directory, download=True)[source]¶

parse_substrates(filename, modifications, accronyms, amino_acids)[source]¶

smpdbParser.py¶

parser(databases_directory, download=True)[source]¶

parsePathways(config, fhandler)[source]¶

parsePathwayProteinRelationships(fhandler)[source]¶

parsePathwayMetaboliteDrugRelationships(fhandler)[source]¶

stringParser.py¶

parser(databases_directory, importDirectory, drug_source=None, download=True, db='STRING')[source]¶

parseActions(databases_directory, importDirectory, proteinMapping, drugMapping=None, download=True, db='STRING')[source]¶

textminingParser.py¶

parser(databases_directory, importDirectory, download=True)[source]¶

read_valid_pubs(organisms, organisms_file)[source]¶

parse_PMC_list(config, directory, download=True, valid_pubs=None)[source]¶

parse_mentions(config, directory, qtype, importDirectory, download=True)[source]¶

uniprotParser.py¶

parser(databases_directory, import_directory, download=True, updated_on=None)[source]¶

parse_release_notes(databases_directory, config, download=True)[source]¶

parse_fasta(databases_directory, config, import_directory, download=True, updated_on=None)[source]¶

parse_idmapping_file(databases_directory, config, import_directory, download=True, updated_on=None)[source]¶

format_output(proteins)[source]¶

print_single_file(data, header, output_file, data_type, data_object, is_first, updated_on)[source]¶

print_multiple_relationships_files(data, header, output_dir, is_first, updated_on)[source]¶

addUniProtTexts(textsFile, proteins)[source]¶

parseUniProtVariants(config, databases_directory, import_directory, download=True, updated_on=None)[source]¶

parseUniProtAnnotations(config, databases_directory, download=True)[source]¶

parseUniProtPeptides(config, databases_directory, download=True)[source]¶