SaveResults.py

import os


class ResultSaver:

    """

    Class to save the results. The output is saved to the temp directory in the data folder if crossmapping is necessary.

    @author: Sebastian Beyvers
    @contact: sebastian.beyvers@med.uni-giessen.de


    """

    def __init__(self, results, organism, wd,  mapped, is_data_dir, out):

        # Constructor and main method for result-saving
        # input_parameter: results     = finished list of gtf-entries
        #                  organism    = input_organism
        #                  wd          = working directory
        #                  mapped      = boolean if crossmapping is necessary
        #                  is_data_dir = boolean if wd is a data_dir (true) or not (false)

        print("Save results to File !")
        self.path = ""

        # If results has to be crossmapped -> Path is tempdirectory.

        if mapped:
            if is_data_dir:
                self.path = os.path.join(wd + "/temp/" + organism + ".gtf")
            else:
                self.path = os.path.join(wd + "/data/temp/" + organism + ".gtf")

        # if no crossmapping is needed:
        else:
            self.path = os.path.join(out)

        with open(self.path, "w") as output_file:
            for line in results:
                output_file.write("\t".join(line)+"\n")