parser.rst

Parser

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.

Public methods

build_ontology_annotations

.. autofunction:: pyhpo.parser.build_ontology_annotations

id_from_string

.. autofunction:: pyhpo.parser.generics.id_from_string

remove_outcommented_rows

.. autofunction:: pyhpo.parser.generics.remove_outcommented_rows

add_decipher_to_term

.. autofunction:: pyhpo.parser.diseases.add_decipher_to_term

add_negative_decipher_to_term

.. autofunction:: pyhpo.parser.diseases.add_negative_decipher_to_term

add_omim_to_term

.. autofunction:: pyhpo.parser.diseases.add_omim_to_term

add_negative_omim_to_term

.. autofunction:: pyhpo.parser.diseases.add_negative_omim_to_term

add_orpha_to_term

.. autofunction:: pyhpo.parser.diseases.add_orpha_to_term

add_negative_orpha_to_term

.. autofunction:: pyhpo.parser.diseases.add_negative_orpha_to_term

all_decipher_diseases

.. autofunction:: pyhpo.parser.diseases.all_decipher_diseases

all_omim_diseases

.. autofunction:: pyhpo.parser.diseases.all_omim_diseases

all_orpha_diseases

.. autofunction:: pyhpo.parser.diseases.all_orpha_diseases

add_gene_to_term

.. autofunction:: pyhpo.parser.genes.add_gene_to_term

all_genes

.. autofunction:: pyhpo.parser.genes.all_genes

terms_from_file

.. autofunction:: pyhpo.parser.obo.terms_from_file

parse_obo_section

.. autofunction:: pyhpo.parser.obo.parse_obo_section