Ensembl.py

from Modules.Ensembl.ActivityTable import ActivityTable
from Modules.Ensembl.FTPHandling.VersionChecker import EnsemblRegulationFTPRetriever as FTPRetriever
from Modules.Ensembl.ActivityCategorizer import ActivityCategorizer
from Modules.Ensembl.GTFGen import GTFGen


class Ensembl:

    """

    Main class for handling Ensembl Regulatory data
    Checks for local files and downloads if files are missing
    @author: Sebastian Beyvers
    @contact: sebastian.beyvers@med.uni-giessen.de

    """

    def __init__(self, organism, wd, data_dir):

        # Constructor and main method for Ensembl-GTF-Creation
        # input_parameter: organism    = input organism
        #                  wd          = working directory
        #                  data_dir    = use data_dir parameter if specified.

        print("Starting Ensembl")
        # Check and Update for Local Ensembl Release Data
        self.updater = FTPRetriever(organism, wd, data_dir)
        self.release = self.updater.get_release()
        # Check for Activitytables (table.bin binary files) and generate if not existing
        self.acttable = ActivityTable(organism, self.release, wd, data_dir)
        self.acttable.check_and_generate_activity_table()
        # Categorize the Activitytable by config defined categories (config: ./config/celltypes_organism.json)
        self.categorizer = ActivityCategorizer(self.release, organism, wd, data_dir)
        print("Generating GTF")
        # Instatiate
        self.gtf_generator = GTFGen(organism, self.release, wd, data_dir)

        print("Ensembl Finished !")

    def get_gtf(self):

        # Getter Method for resulting GTF-Entries as List.
        # return_value: list of gtf entries.

        return self.gtf_generator.get_gtf(self.release, self.categorizer.get_categorization())

#e = Ensembl("homo_sapiens")
#print(len(e.categorizer.categorization))