"""
Pre-loaded example dataset for PyModulon tutorials.
"""
from os import path
import pandas as pd
from pymodulon.io import load_json_model
[docs]_data_dir = path.join(path.abspath(path.dirname(__file__)), "data")
[docs]_ecoli_dir = path.join(_data_dir, "ecoli")
# E. coli datasets
[docs]M = pd.read_csv(path.join(_ecoli_dir, "M.csv"), index_col=0)
[docs]A = pd.read_csv(path.join(_ecoli_dir, "A.csv"), index_col=0)
[docs]X = pd.read_csv(path.join(_ecoli_dir, "X.csv"), index_col=0)
[docs]gene_table = pd.read_csv(path.join(_ecoli_dir, "gene_table.csv"), index_col=0)
[docs]sample_table = pd.read_csv(path.join(_ecoli_dir, "sample_table.csv"), index_col=0)
[docs]imodulon_table = pd.read_csv(path.join(_ecoli_dir, "imodulon_table.csv"), index_col=0)
[docs]trn = pd.read_csv(path.join(_ecoli_dir, "trn.csv"), index_col=None)
# E. coli genome annotations
[docs]ecoli_fasta = path.join(_ecoli_dir, "genome.fasta")
[docs]ecoli_gff = path.join(_ecoli_dir, "genome.gff3")
[docs]ecoli_eggnog = path.join(_ecoli_dir, "eggNOG_annotations.txt")
[docs]ecoli_biocyc = path.join(_ecoli_dir, "biocyc_operon_annotations.txt")
[docs]ecoli_go_example = path.join(_ecoli_dir, "GO_example_annotations.txt")
# Load E coli IcaData Object
[docs]def load_ecoli_data():
"""
Load *Escherichia coli* :class:`~pymodulon.core.IcaData` object from
:cite:`Sastry2019`
Returns
-------
ecoli_data: ~pymodulon.core.IcaData
*E. coli* :class:`~pymodulon.core.IcaData` object
"""
return load_json_model(path.join(_data_dir, "objects", "ecoli_data.json.gz"))
[docs]def load_staph_data():
"""
Load *Staphylococcus aureus* :class:`~pymodulon.core.IcaData` object from
:cite:`Poudel2020`
Returns
-------
staph_data: ~pymodulon.core.IcaData
*S. aureus* :class:`~pymodulon.core.IcaData` object
"""
return load_json_model(path.join(_data_dir, "objects", "staph_data.json.gz"))
[docs]def load_bsub_data():
"""
Load *Bacillus subtilis* :class:`~pymodulon.core.IcaData` object from
:cite:`Rychel2020a`
Returns
-------
bsub_data: ~pymodulon.core.IcaData
*B. subtilis* :class:`~pymodulon.core.IcaData` object
"""
return load_json_model(path.join(_data_dir, "objects", "bsub_data.json.gz"))
[docs]def load_example_bbh():
"""
Load an example bi-directional blast best hit (BBH) file
Returns
-------
example_bbh: ~pandas.DataFrame
Example BBH file
"""
return pd.read_csv(path.join(_data_dir, "bbh", "example_bbh.csv"), index_col=0)
[docs]def load_example_log_tpm():
"""
Load an example expression dataset in units log-TPM
Returns
-------
example_tpm: ~pandas.DataFrame
Example expression dataset
"""
return pd.read_csv(path.join(_data_dir, "ecoli", "example_tpm.csv"), index_col=0)