Source code for validation.ecoli.validation_data_raw

"""
ValidationDataRawEcoli

Raw validation data for Ecoli. Contains raw data processed
directly from TSV flat files.
"""

import os
from reconstruction.spreadsheets import read_tsv

FLAT_DIR = os.path.join(os.path.dirname(__file__), "flat")
LIST_OF_DICT_FILENAMES = (
    "amino_acid_growth_rates.tsv",
    "amino_acid_growth_rates_dose_response.tsv",
    "essential_genes.tsv",
    "geneFunctions.tsv",
    "houser2015_javier_table.tsv",
    "li_protein_synthesis_rates_2014.tsv",
    "macromolecular_growth_rate_modulation.tsv",
    "schmidt2015_javier_table.tsv",
    "taniguichi2010_table_6.tsv",
    "toya_2010_central_carbon_fluxes.tsv",
    "wisniewski2014_supp2.tsv",
)




class ValidationDataRawEcoli(object):
    """ValidationDataRawEcoli"""

    def __init__(self):
        """Load raw data from TSV files"""
        for filename in LIST_OF_DICT_FILENAMES:
            self._load_tsv(os.path.join(FLAT_DIR, filename))



    def _load_tsv(self, file_name):
        attrName = file_name.split(os.path.sep)[-1].split(".")[0]
        setattr(self, attrName, [])

        rows = read_tsv(file_name)
        setattr(self, attrName, rows)