Module hetmatpy.testing

None

None

View Source

import json

import hetnetpy.readwrite

import hetmatpy.hetmat

format_github_url = "https://github.com/{repo_slug}/raw/{commit}/{path}".format

hetnet_urls = {

    # Figure 2D of Himmelstein & Baranzini

    # (2015) PLOS Comp Bio. https://doi.org/10.1371/journal.pcbi.1004259.g002

    "disease-gene-example": format_github_url(

        repo_slug="hetio/hetnetpy",

        commit="9dc747b8fc4e23ef3437829ffde4d047f2e1bdde",

        path="test/data/disease-gene-example-graph.json",

    ),

    # The bupropion and nicotine dependence Hetionet v1.0 subgraph.

    "bupropion-subgraph": format_github_url(

        repo_slug="hetio/hetnetpy",

        commit="30c6dbb18a17c05d71cb909cf57af7372e4d4908",

        path="test/data/bupropion-CbGpPWpGaD-subgraph.json.xz",

    ),

    # A random Hetionet v1.0 subgraph.

    "random-subgraph": format_github_url(

        repo_slug="hetio/hetnetpy",

        commit="30c6dbb18a17c05d71cb909cf57af7372e4d4908",

        path="test/data/random-subgraph.json.xz",

    ),

}

hetnet_io_cache = {}

def get_graph(name, hetmat=False, directory=None):

    """

    If hetmat=True, import graph into a hetmat located on-disk at directory.

    """

    if name not in hetnet_urls:

        raise ValueError(

            f"{name} is not a supported test hetnet.\n"

            "Choose from the following currently defined hetnets: "

            + ", ".join(hetnet_urls)

        )

    if name not in hetnet_io_cache:

        url = hetnet_urls[name]

        read_file = hetnetpy.readwrite.open_read_file(url, text_mode=True)

        hetnet_io_cache[name] = read_file.read()

    writable = json.loads(hetnet_io_cache[name])

    graph = hetnetpy.readwrite.graph_from_writable(writable)

    if not hetmat:

        return graph

    assert directory is not None

    hetmat = hetmatpy.hetmat.hetmat_from_graph(graph, directory)

    return hetmat

Variables

hetnet_io_cache

hetnet_urls

Functions

format_github_url

def format_github_url(
    ...
)

S.format(args, *kwargs) -> str

Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces ('{' and '}').

get_graph

def get_graph(
    name,
    hetmat=False,
    directory=None
)

If hetmat=True, import graph into a hetmat located on-disk at directory.

View Source

def get_graph(name, hetmat=False, directory=None):

    """

    If hetmat=True, import graph into a hetmat located on-disk at directory.

    """

    if name not in hetnet_urls:

        raise ValueError(

            f"{name} is not a supported test hetnet.\n"

            "Choose from the following currently defined hetnets: "

            + ", ".join(hetnet_urls)

        )

    if name not in hetnet_io_cache:

        url = hetnet_urls[name]

        read_file = hetnetpy.readwrite.open_read_file(url, text_mode=True)

        hetnet_io_cache[name] = read_file.read()

    writable = json.loads(hetnet_io_cache[name])

    graph = hetnetpy.readwrite.graph_from_writable(writable)

    if not hetmat:

        return graph

    assert directory is not None

    hetmat = hetmatpy.hetmat.hetmat_from_graph(graph, directory)

    return hetmat