Annotations¶
The Annotations
section contains various metadata annotations for HPO terms.
GeneSingleton
class¶
-
class
pyhpo.annotations.
GeneSingleton
(idx: Optional[int], name: str)[source]¶ This class represents a single gene.
Note
GeneSingleton
should never be initiated directly, but only viaGeneDict
to ensure that every gene is only created once.-
id
¶ HGNC gene ID
- Type
int
-
name
¶ HGNC gene synbol
- Type
str
-
symbol
¶ HGNC gene symbol (alias of
GeneSingleton.name
)- Type
str
-
hpo
¶ all HPOTerms associated to the gene
- Type
set of
pyhpo.term.HPOTerm
- Parameters
idx (int) – HGNC gene ID
name (str) – HGNC gene synbol
-
toJSON¶
-
GeneSingleton.
toJSON
(verbose: bool = False) → Dict[source]¶ JSON (dict) representation of
Gene
- Parameters
verbose (bool, default:
False
) – Return all associated HPOTerms- Returns
A dict with the following keys
id - The HGNC ID
name - The gene symbol
symbol - The gene symbol (same as
name
)hpo - (If
verbose == True
): set ofpyhpo.term.HPOTerm
- Return type
dict
GeneDict
class¶
-
class
pyhpo.annotations.
GeneDict
[source]¶ An associative dict of all genes
Ensures that every gene is a single GeneSingleton instance and no duplicate instances are generated during parsing of the Gen-Pheno-HPO associations.
This class is initilized once and genes are created by calling the instance of GeneDict to ensure that the same gene exists only once.
For example
Gene = GeneDict() gba = Gene(symbol='GBA') ezh2 = Gene(symbol='EZH2') gba_2 = Gene(symbol='GBA') gba is ezh2 >> False gba is gba_2 >> True
- Parameters
cols (list, default:
None
) –Only used for backwards compatibility reasons. Should have the following entries
None
None
HGNC-ID
Gene symbol
hgncid (int) – The HGNC ID
symbol (str) – The gene symbol (alternative to name)
- Returns
- Return type
DiseaseSingleton
class¶
-
class
pyhpo.annotations.
DiseaseSingleton
(idx: int, name: str)[source]¶ This class represents a single disease.
Note
DiseaseSingleton
should never be initiated directly, but only via the appropriate disease dictionary, e.g.OmimDict
(DiseaseDict
) to ensure that every disease is only created once.-
id
¶ Disease ID
- Type
int
-
name
¶ disease name
- Type
str
-
hpo
¶ all HPOTerms associated to the disease
- Type
set of
pyhpo.term.HPOTerm
- Parameters
idx (int) – Disease ID
name (str) – Disease name
-
toJSON¶
-
DiseaseSingleton.
toJSON
(verbose: bool = False) → Dict[source]¶ JSON (dict) representation of
Disease
- Parameters
verbose (bool, default:
False
) – Return all associated HPOTerms- Returns
A dict with the following keys
id - The Disease ID
name - The disease name
hpo - (If
verbose == True
): set ofpyhpo.term.HPOTerm
- Return type
dict
DiseaseDict
class¶
-
class
pyhpo.annotations.
DiseaseDict
[source]¶ An associative dict of all Omim Diseases
Ensures that every Omim Disease is a single OmimDisease instance and no duplicate instances are generated during parsing of the Gen-Pheno-HPO associations.
This class is initilized once and diseases are created by calling the instance of
DiseaseDict
to ensure that the same disease exists only once.For example
Disease = OmimDict() gaucher = Disease(diseaseid=1) fabry = Disease(diseaseid=2) gaucher_2 = Disease(diseaseid=1) gaucher is fabry >> False gaucher is gaucher_2 >> True
- Parameters
cols (list, default:
None
) –Only used for backwards compatibility reasons. Should have the following entries
None
Disease ID
Disease Name
diseaseid (int) – The Disease ID
name (str) – The disease name
- Returns
- Return type
Omim¶
Instance of pyhpo.annotations.DiseaseDict
to handle Omim diseases. Ensures that diseases are not duplicated through use of Singletons.
Orpha¶
Instance of pyhpo.annotations.DiseaseDict
to handle Orphanet diseases. Ensures that diseases are not duplicated through use of Singletons.
Decipher¶
Instance of pyhpo.annotations.DiseaseDict
to handle Decipher diseases. Ensures that diseases are not duplicated through use of Singletons.
HPO_Gene
class¶
Methods¶
parse_pheno_file¶
-
pyhpo.annotations.
parse_pheno_file
(filename: Optional[str] = None, path: str = './', delimiter: str = '\t') → Tuple[Any, …][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: Iterator[str], ignorechar: str = '#') → Iterator[str][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