The parser
section contains functions to parse the master data,
such as hpo.obo
and phenotype...
files. These methods should
mostly be left untouched and there is very little need for client-side
code to interact with these methods. The documentation here is mostly
for developers of the library.
.. autofunction:: pyhpo.parser.build_ontology_annotations
.. autofunction:: pyhpo.parser.generics.id_from_string
.. autofunction:: pyhpo.parser.generics.remove_outcommented_rows
.. autofunction:: pyhpo.parser.diseases.add_decipher_to_term
.. autofunction:: pyhpo.parser.diseases.add_negative_decipher_to_term
.. autofunction:: pyhpo.parser.diseases.add_omim_to_term
.. autofunction:: pyhpo.parser.diseases.add_negative_omim_to_term
.. autofunction:: pyhpo.parser.diseases.add_orpha_to_term
.. autofunction:: pyhpo.parser.diseases.add_negative_orpha_to_term
.. autofunction:: pyhpo.parser.diseases.all_decipher_diseases
.. autofunction:: pyhpo.parser.diseases.all_omim_diseases
.. autofunction:: pyhpo.parser.diseases.all_orpha_diseases
.. autofunction:: pyhpo.parser.genes.add_gene_to_term
.. autofunction:: pyhpo.parser.genes.all_genes
.. autofunction:: pyhpo.parser.obo.terms_from_file
.. autofunction:: pyhpo.parser.obo.parse_obo_section