Source code for micom.data

"""Submodule including some common data sets."""

from ..workflows import load_results
from os.path import split, join
from numpy.random import randint
import pandas as pd
import pickle

__all__ = ("agora", "test_taxonomy")
this_dir, _ = split(__file__)



agora = pd.read_csv(join(this_dir, "agora.csv"))

agora["file"] = agora["id"] + ".xml"

test_db = join(this_dir, "artifacts", "species_models.qza")
test_medium = join(this_dir, "artifacts", "medium.qza")




def test_taxonomy(n=4):
    """Create a simple test taxonomy.

    Parameters
    ----------
    n : positive int
        How many species to include.

    Returns
    -------
    pandas.DataFrame
        Taxonomy specification for a.

    """
    ecoli_file = join(this_dir, "e_coli_core.xml.gz")
    ids = ["Escherichia_coli_{}".format(i) for i in range(1, n + 1)]
    taxa = pd.DataFrame({"id": ids})
    taxa["genus"] = "Escherichia"
    taxa["species"] = "Escherichia coli"
    taxa["reactions"] = 95
    taxa["metabolites"] = 72
    taxa["file"] = ecoli_file
    return taxa



def test_data(n_samples=4, uses_db=True):
    """Create a simple test data set.

    Parameters
    ----------
    n_samples : positive int
        How many samples to include.
    uses_db : bool
        Whether the data is used with a model database.

    Returns
    -------
    pandas.DataFrame
        Taxonomy specification for the example data.

    """
    samples = ["sample_%d" % i for i in range(1, n_samples + 1)]
    data = [test_taxonomy() for s in samples]
    for i, d in enumerate(data):
        d["sample_id"] = samples[i]
        d["species"] += " " + d.index.astype("str")
    data = pd.concat(data)
    data["abundance"] = randint(1, 1000, data.shape[0])
    if uses_db:
        del data["file"]
    return data


def test_results():
    """Return growth results for a realistic example data sets.

    This will give you access to the results as produced by the community tutorial
    at https://github.com/micom-dev/q2-micom/tree/main/docs.

    Returns
    -------
    GrowthResults
        The results for running the `grow` workflow with a tradeoff of 0.8.
    """
    return load_results(join(this_dir, "artifacts", "results.zip"))


def test_tradeoff():
    """Return tradeoff results for a realistic example data set.

    This will give you access to the tradeoffs as produced by the community tutorial
    at https://github.com/micom-dev/q2-micom/tree/main/docs.

    Returns
    -------
    pandas.DataFrame
        Growth rates for varying tradeoff values.
    """
    return pd.read_csv(join(this_dir, "artifacts", "crc_tradeoff.csv"), index_col=0)