Commit 1ba3eff4 authored by jedlickap's avatar jedlickap
Browse files

add updated scripts

parent 343f63fc

nested/core/tools/retro_te_domains.py

+6 −2
Original line number Diff line number Diff line
@@ -37,7 +37,7 @@ class RetroTeDomains(ToolInterface): 
        

        retro_domains = self._filter_candidates(candidates)



        retro_domains.sort(key=lambda e: e.location[0])

        retro_domains.sort(key=lambda e: e.location[0], reverse=True)

        self.output_object = RetroDomainOutputObject(self.seqId, sequence, retro_domains)

        return retro_domains
@@ -45,8 +45,12 @@ class RetroTeDomains(ToolInterface): 
        retro_domains = []

        # filter on matches with evalue 0.1 and lower

        candidates = [candidate for candidate in candidates if candidate.evalue <= 0.1]

        

        for c in candidates:

            c.location.sort()

        

        # sort after location and score

        candidates.sort(key=lambda e: (e.location, -e.score))

        candidates.sort(key=lambda e: (e.location[0], -e.score))

        for candidate in candidates:

            add = True

            for domain in retro_domains:

nested/output/output_generators/retro_domain_output_generator.py

+5 −1
Original line number Diff line number Diff line
@@ -12,6 +12,11 @@ class RetroDomainOutputGenerator(BaseOutputGenerator): 
    def generate_output(self, output_object: RetroDomainOutputObject) -> NoReturn:

        self.create_data_directory(output_object.sequence_id)

        

        # sort elements after location[0]

        for element in output_object.elements:

            element.location = [min(element.location), max(element.location)]

        output_object.elements.sort(key=lambda e: e.location[0])



        with open(f"{self.directory}/{output_object.sequence_id}/{output_object.sequence_id}_retro_domain.gff", "w+") as gff:

            i = 0

            gff.write("##gff-version 3\n")
@@ -20,7 +25,6 @@ class RetroDomainOutputGenerator(BaseOutputGenerator): 
                sign = (lambda x: x and (1, -1)[x < 0])(domain.frame[0])

                strand = "+"

                if sign < 0:

                    domain_location = [domain_location[1], domain_location[0]]

                    strand = '-'                

                gff.write(output_object.sequence_id + "\t"

                          + "retroTeDomain\tpolypeptide_conserved_region\t"

nested/core/executor.py

+2 −2

File changed.

Contains only whitespace changes.