Commit 42b4e318 authored by jedlickap's avatar jedlickap
Browse files

trf fix

parent 3dafa070

nested/core/nester.py

+2 −2
Original line number Original line Diff line number Diff line
@@ -43,9 +43,9 @@ class Nester(ToolInterface): 
        

        

        nested_list += self._get_unexpanded_transposon_list(cropped_sequence, self.threshold)  # find list of nested transposons

        nested_list += self._get_unexpanded_transposon_list(cropped_sequence, self.threshold)  # find list of nested transposons

        nested_list = self._expand_transposon_list(nested_list)

        nested_list = self._expand_transposon_list(nested_list)

        print(len(nested_list))



        nested_list = self._filter_nested_list(nested_list)

        nested_list = self._filter_nested_list(nested_list)

        print(len(nested_list))       

     

        self.nested_element = NestedElement(self.seqid, self.sequence, nested_list)

        self.nested_element = NestedElement(self.seqid, self.sequence, nested_list)

        

        

    def _get_unexpanded_transposon_list(self, sequence, threshold):

    def _get_unexpanded_transposon_list(self, sequence, threshold):

nested/core/tandem_repeat.py

+3 −3
Original line number Original line Diff line number Diff line
@@ -75,7 +75,7 @@ def get_candidates(seqid): 
            candidates.append(TandemRepeat([int(split[0]), int(split[1])], int(split[2]), float(split[3]),

            candidates.append(TandemRepeat([int(split[0]), int(split[1])], int(split[2]), float(split[3]),

                    int(split[5]), int(split[6]), int(split[7]), float(split[12]), split[-1]))

                    int(split[5]), int(split[6]), int(split[7]), float(split[12]), split[-1]))





    cleanup()

    cleanup(seqid)

    

    

    return candidates

    return candidates
@@ -104,7 +104,7 @@ def filter_candidates(candidates): 
            repeats.append(candidate)

            repeats.append(candidate)

    return repeats

    return repeats





def cleanup():

def cleanup(seqid):

    if os.path.isfile("{}.fa.2.5.7.80.10.50.2000.dat".format(seqid)):

    if os.path.isfile("{}.fa.2.5.7.80.10.50.2000.dat".format(seqid)):

        os.remove("{}.fa.2.5.7.80.10.50.2000.dat".format(seqid))

        os.remove("{}.fa.2.5.7.80.10.50.2000.dat".format(seqid))

    if os.path.isfile("{}.fa.2.5.7.80.10.50.2000.mask".format(seqid)):

    if os.path.isfile("{}.fa.2.5.7.80.10.50.2000.mask".format(seqid)):