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