InterPro#

class openomics.database.ontology.InterPro(path='https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/', index_col='UniProtKB-AC', keys=None, file_resources=None, col_rename=None, **kwargs)[source][source]#

Bases: openomics.database.ontology.Ontology

Default parameters path=”https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/” file_resources = {

“entry.list”: “entry.list”, “protein2ipr.dat.gz”: “protein2ipr.dat.gz”, “interpro2go”: “interpro2go”, “ParentChildTreeFile.txt”: “ParentChildTreeFile.txt”,

}

Methods Summary

`load_annotation`(file_resources[, blocksize])
`load_dataframe`(file_resources[, blocksize])	Handles data preprocessing given the file_resources input, and returns a DataFrame.
`load_network`(file_resources)	rtype `Tuple`[`Graph`, `ndarray`]
`parse_interpro2go`(file)	rtype `DataFrame`
`parse_ipr_treefile`(lines)	Parse the InterPro Tree from the given file.

Methods Documentation

load_annotation(file_resources, blocksize=None)[source][source]#

load_dataframe(file_resources, blocksize=None)[source][source]#

Handles data preprocessing given the file_resources input, and returns a DataFrame.

Parameters

file_resources (dict) – A dict with keys as filenames and values as full file path.
blocksize (int) –

load_network(file_resources)[source][source]#

Return type: Tuple[Graph, ndarray]

parse_interpro2go(file)[source][source]#

Return type: DataFrame

parse_ipr_treefile(lines)[source][source]#

Parse the InterPro Tree from the given file. :param lines: A readable file or file-like

Return type: MultiDiGraph