bioflow.bio_db_parsers package¶
Submodules¶
bioflow.bio_db_parsers.ComplexPortalParser module¶
bioflow.bio_db_parsers.PhosphositeParser module¶
bioflow.bio_db_parsers.geneOntologyParser module¶
Contains the functions responsible for the parsing of the GO terms
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class
bioflow.bio_db_parsers.geneOntologyParser.
GOTermsParser
[source]¶ Bases:
object
Wrapper object for a parser of GO terms.
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parse_go_terms
(source_file_path)[source]¶ Takes the path to the gene ontology .obo file and returns result of parse dict and list
Parameters: source_file_path – gene ontology .obo file Returns: dict containing term parse, list containing inter-term relationship (turtle) triplets
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bioflow.bio_db_parsers.proteinRelParsers module¶
Protein relationships parser
bioflow.bio_db_parsers.reactomeParser module¶
bioflow.bio_db_parsers.tfParsers module¶
bioflow.bio_db_parsers.uniprotParser module¶
The module responsible for parsing of the Uniprot SWISSPROT .dat file for a subset of cross-references that are useful in our database.
Once uniprot is parsed, it is returned as the dictionary containing the following elements:
- Uniprot = { SWISSPROT_ID:{
- ‘Acnum’:[], ‘Names’: {‘Full’: ‘’, ‘AltNames’: []}, ‘GeneRefs’: {‘Names’: [], ‘OrderedLocusNames’: [], ‘ORFNames’: []}, ‘TaxID’: ‘’, ‘Ensembl’: [], ‘KEGG’: [], ‘EMBL’: [], ‘GO’: [], ‘Pfam’: [], ‘SUPFAM’: [], ‘PDB’: [], ‘GeneID’: [], }}
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class
bioflow.bio_db_parsers.uniprotParser.
UniProtParser
(tax_ids_to_parse)[source]¶ Bases:
object
Wraps the Uniprot parser
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get_access_dicts
()[source]¶ Returns an access dictionary that would plot genes names, AcNums or EMBL identifiers to the Swissprot IDs
Returns: dictionary mapping all teh external database identifiers towards uniprot IDs
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parse_gene_references
(line)[source]¶ Parses gene names and references from the UNIPROT text file
Parameters: line –
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parse_name
(line)[source]¶ Parses a line that contains a name associated to the entry we are trying to load
Parameters: line – Returns:
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parse_uniprot
(source_path)[source]¶ Performs the entire uniprot file parsing and importing
Parameters: source_path – path towards the uniprot test file Returns: uniprot parse dictionary
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