drive.models package#
Submodules#
drive.models.data_container module#
- class drive.models.data_container.Data(networks: List[Network_Interface], output_path: Path, carriers: Dict[str, Dict[str, Set[str]]], phenotype_descriptions: Dict[str, Dict[str, str]])[source]#
Bases:
objectmain class to hold the data from the network analysis and the different pvalues
- carriers: Dict[str, Dict[str, Set[str]]]#
- networks: List[Network_Interface]#
- output_path: Path#
- phenotype_descriptions: Dict[str, Dict[str, str]]#
- class drive.models.data_container.Data_Interface(*args, **kwargs)[source]#
Bases:
ProtocolProtocol defining what attributes the DataHolder Interface needs to have
- carriers: Dict[str, Dict[str, Set[str]]]#
- networks: List[Network_Interface]#
- output_path: Path#
- phenotype_descriptions: Dict[str, Dict[str, str]]#
drive.models.generate_indices module#
- class drive.models.generate_indices.Germline(id1_indx: int = 0, hap1_indx: int = 1, id2_indx: int = 2, hap2_indx: int = 3, chr_indx: int = 4, str_indx: int = 5, end_indx: int = 6, cM_indx: int = 10, unit: int = 11)[source]#
Bases:
FileIndices- cM_indx: int = 10#
- chr_indx: int = 4#
- end_indx: int = 6#
- get_haplotype_id(data: DataFrame, ind_id_indx: int, phase_col_indx: int, col_name: str) None[source]#
- hap1_indx: int = 1#
- hap2_indx: int = 3#
- id1_indx: int = 0#
- id2_indx: int = 2#
- str_indx: int = 5#
- unit: int = 11#
- class drive.models.generate_indices.HapIBD(id1_indx: int = 0, hap1_indx: int = 1, id2_indx: int = 2, hap2_indx: int = 3, chr_indx: int = 4, str_indx: int = 5, end_indx: int = 6, cM_indx: int = 7)[source]#
Bases:
FileIndices- cM_indx: int = 7#
- chr_indx: int = 4#
- end_indx: int = 6#
- get_haplotype_id(data: DataFrame, ind_id_indx: int, phase_col_indx: int, col_name: str) None[source]#
- hap1_indx: int = 1#
- hap2_indx: int = 3#
- id1_indx: int = 0#
- id2_indx: int = 2#
- str_indx: int = 5#
- class drive.models.generate_indices.Rapid(id1_indx: int = 1, hap1_indx: int = 3, id2_indx: int = 2, hap2_indx: int = 4, chr_indx: int = 0, cM_indx: int = 7, str_indx: int = 5, end_indx: int = 6)[source]#
Bases:
FileIndices- cM_indx: int = 7#
- chr_indx: int = 0#
- end_indx: int = 6#
- get_haplotype_id(data: DataFrame, ind_id_indx: int, phase_col_indx: int, col_name: str) None[source]#
- hap1_indx: int = 3#
- hap2_indx: int = 4#
- id1_indx: int = 1#
- id2_indx: int = 2#
- str_indx: int = 5#
- drive.models.generate_indices.create_indices(ibd_file_format: str) FileIndices[source]#
Factory method to generate the proper file indice object based on the ibd program
- Parameters:
ibd_file_format (str) – string indicating what ibd program was used identify IBD segments. EX: hapibd, ilash, rapid, and germline. expects this value to be lower case
- Returns:
returns an object that conforms to the FileIndices protocol. It will have the method getHAPID. It will also have the correct indices for the ibd program
- Return type:
- Raises:
ValueError – Raises a value error if the user passes an ibd_file_format that is not hapibd, hap-ibd, germline, ilash, rapid
- class drive.models.generate_indices.iLASH(id1_indx: int = 0, hap1_indx: int = 1, id2_indx: int = 2, hap2_indx: int = 3, chr_indx: int = 4, str_indx: int = 5, end_indx: int = 6, cM_indx: int = 9)[source]#
Bases:
FileIndices- cM_indx: int = 9#
- chr_indx: int = 4#
- end_indx: int = 6#
- get_haplotype_id(data: DataFrame, ind_id_indx: int, phase_col_indx: int, col_name: str) None[source]#
- hap1_indx: int = 1#
- hap2_indx: int = 3#
- id1_indx: int = 0#
- id2_indx: int = 2#
- str_indx: int = 5#
drive.models.networks module#
- class drive.models.networks.Network(clst_id: float, true_positive_count: int, true_positive_percent: float, false_negative_edges: List[int], false_negative_count: int, members: Union[Set[int], Set[str]], haplotypes: Union[List[int], List[str]], min_pvalue_str: str = '', pvalues: Dict[str, Dict[str, Any]] = <factory>)[source]#
Bases:
object- clst_id: float#
- false_negative_count: int#
- false_negative_edges: List[int]#
- haplotypes: List[int] | List[str]#
- members: Set[int] | Set[str]#
- min_pvalue_str: str = ''#
- print_members_list() str[source]#
Returns a string that has all of the members ids separated by space
- Returns:
returns a string where the members list attribute is formatted as a string for the output file. Individuals strings are joined by comma.
- Return type:
str
- pvalues: Dict[str, Dict[str, Any]]#
- true_positive_count: int#
- true_positive_percent: float#
- class drive.models.networks.Network_Interface(*args, **kwargs)[source]#
Bases:
Protocol- clst_id: float#
- false_negative_count: int#
- false_negative_edges: List[int]#
- haplotypes: List[int]#
- members: Set[int]#
- min_pvalue_str: str = ''#
- print_members_list() str[source]#
Returns a string that has all of the members ids separated by space
- Returns:
returns a string where the members list attribute is formatted as a string for the output file. Individuals strings are joined by comma.
- Return type:
str
- pvalues: Dict[str, str] = Field(name=None,type=None,default=<dataclasses._MISSING_TYPE object>,default_factory=<class 'dict'>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=<dataclasses._MISSING_TYPE object>,_field_type=None)#
- true_positive_count: int#
- true_positive_percent: float#