Commit 6fc973ec authored by Pavel Jedlicka's avatar Pavel Jedlicka
Browse files

fixed chromo domain overlap with ltr

parent 41a0a417

nested/core/nester.py

+1 −1
Original line number Diff line number Diff line
@@ -87,8 +87,8 @@ class Nester(object): 
        return nested_list



    def _expand_transposon_list(self, nested_list):

        # backwards expanding of intervals according to previously found and cropped elements

        for i in reversed(range(len(nested_list) - 1)):

        # backwards expanding of intervals according to previously found and cropped elements

            for j in range(i + 1, len(nested_list)):

                nested_list[j].location = intervals.expand(nested_list[i].location, nested_list[j].location)

                nested_list[j].ltr_left_location = intervals.expand(nested_list[i].location,

nested/scoring/graph.py

+2 −2
Original line number Diff line number Diff line
@@ -83,8 +83,8 @@ class Graph(object): 
        for domain in domain_list:

            if domain.type not in ['GAG', 'PROT', 'INT', 'RT', 'RH', 'aRH', 'CHD', 'CHDCR']:

                continue

            if (intervals.compare(te.ltr_left_location, domain.location) != 1

              and intervals.compare(domain.location, te.ltr_right_location) != 1):

            if (intervals.compare(te.ltr_left_location, sorted(domain.location)) != 1

              and intervals.compare(sorted(domain.location), te.ltr_right_location) != 1):

                domain_dict[domain.type].append(domain)

                i += 1

        i = 0