Annotations¶
The Annotations
section contains various metadata annotations for HPO terms.
Gene
class¶
HPO_Gene
class¶
Methods¶
parse_pheno_file¶
-
pyhpo.annotations.
parse_pheno_file
(filename=None, path='./', delimiter='\t')[source]¶ Parses OMIM-HPO assoation file and generates a positive and negative annotation dictionary
Parameters: - filename (str) – Filename of HPO-Gene association file. Defaults to filename from HPO
- path (str) – Path to data files. Defaults to ‘./’
Returns: - omim_dict (dict) – Dictionary containing all HPO-OMIM associations. HPO-ID is the key
- negative_omim_dict (dict) – Dictionary containing all negative HPO-OMIM associations. HPO-ID is the key
remove_outcommented_rows¶
-
pyhpo.annotations.
remove_outcommented_rows
(fh, ignorechar='#')[source]¶ Removes all rows from a filereader object that start with a comment character
Parameters: - fh (iterator) – any object which supports the iterator protocol and returns a string each time its __next__() method is called — file objects and list objects are both suitable
- ignorechar (str, defaults:
#
) – All lines starting with this character will be ignored
Yields: row (str) – One row of the
fh
iterator