Uniquifier.py

class UniqueFilter:
    """

    Class to get unique GTF-results, filtered by specified cell-/tissuetypes

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

    """

    def __init__(self, ense, ucsc, org_filter=None):

        # Constructor
        # input_parameter: ense = list of gtf-formatted entries from Ensembl data
        #                  ucsc = list of gtf-formatted entries from UCSC data
        #                  org_filter = filter for specific celltype

        self.results = self.get_filtered_results(org_filter, ense, ucsc)

    def get_results(self):

        # Getter method for results variable

        return self.results

    def get_filtered_results(self, org_filter, ense, ucsc):

        # Method to concat ucsc and ensemble dataset without duplicates and filter by activitylist
        # input_parameter: ense = list of gtf-formatted entries from Ensembl data
        #                  ucsc = list of gtf-formatted entries from UCSC data
        #                  org_filter = filter for specific celltype
        # return_value: List of unique (filtered) results.

        unfiltered_results = self.concat_without_duplicates(ense, ucsc)  # First: Concat ucsc and ensembl data
        if org_filter:                                                   # Second: apply filter if specified
            filterstrings = [x+">ACTIVE" for x in org_filter]
            return_list = []
            for element in unfiltered_results:
                if any(tissue in element[-1] for tissue in filterstrings):
                    return_list.append(element)
            return return_list
        else:
            return unfiltered_results


    @staticmethod
    def concat_without_duplicates(ense, ucsc):

        # Concat UCSC and Ensembl data without duplicates
        # input_parameter: ense = ensembl-gtf-data and ucsc = ucsc-gtf-data
        # return_value: concatinated list of gtf-entries without duplicates

        results = ense+ucsc
        for ens in ense:
            for uc in ucsc:
                if ens[0] == uc[0]:
                    #print("Chromosome Equal")
                    if ense[3] == uc[3]:
                        results.remove(ucsc)

        return results