Commit 564cd5b1 authored by Pavel Jedlicka's avatar Pavel Jedlicka
Browse files

added flag for solo ltrs

parent fa95fb13

nested/cli/nester.py

+9 −5
Original line number Original line Diff line number Diff line
@@ -27,8 +27,9 @@ from nested.utils.dependency_resolver import DependencyResolver 
@click.option('--discovery_tool', '-dt', default=DiscoveryTool.LTR_finder.name,

@click.option('--discovery_tool', '-dt', default=DiscoveryTool.LTR_finder.name,

    type=click.Choice(list(map(lambda val: val, DiscoveryTool.__members__))),

    type=click.Choice(list(map(lambda val: val, DiscoveryTool.__members__))),

    help='Determines which tool is used for retrotransoson discovery. Default: LTR_finder')

    help='Determines which tool is used for retrotransoson discovery. Default: LTR_finder')

@click.option('--solo_ltrs', '-solo', is_flag=True, default=False, help='Run solo LTR module')

def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initial_threshold, 

def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initial_threshold, 

        threshold_multiplier, threads, discovery_tool):

        threshold_multiplier, threads, discovery_tool, solo_ltrs):

    check_ram(input_fasta, threads)

    check_ram(input_fasta, threads)

    check_permissions(output_folder, os.W_OK | os.X_OK)

    check_permissions(output_folder, os.W_OK | os.X_OK)

    number_of_errors = [0]

    number_of_errors = [0]
@@ -41,21 +42,24 @@ def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initia 
            futuress.append(executor.submit(process_sequence, sequence, sketcher, 

            futuress.append(executor.submit(process_sequence, sequence, sketcher, 

                sketch, format, output_fasta_offset, output_folder, 

                sketch, format, output_fasta_offset, output_folder, 

                initial_threshold, threshold_multiplier, number_of_errors,

                initial_threshold, threshold_multiplier, number_of_errors,

                dependencyResolver))

                dependencyResolver, solo_ltrs))

        futures.wait(futuress)

        futures.wait(futuress)

    end_time = datetime.now()

    end_time = datetime.now()

    print('Total time: {}'.format(end_time - start_time))

    print('Total time: {}'.format(end_time - start_time))

    print('Number of errors: {}'.format(number_of_errors[0]))

    print('Number of errors: {}'.format(number_of_errors[0]))





def process_sequence(sequence, sketcher, sketch, format, output_fasta_offset, output_folder, initial_threshold, threshold_multiplier, errors, dependency_resolver):

def process_sequence(sequence, sketcher, sketch, format, output_fasta_offset, output_folder, initial_threshold, threshold_multiplier, errors, dependency_resolver, solo_ltrs):

    sequence.id = sequence.id.replace('/', '--')

    sequence.id = sequence.id.replace('/', '--')

    seq_start_time = datetime.now()

    seq_start_time = datetime.now()

    strlen = 15

    strlen = 15

    print("Processing {}".format(sequence.id))

    print("Processing {}".format(sequence.id))

    try:

    try:

        nester = Nester(sequence, initial_threshold, threshold_multiplier, dependency_resolver)

        nester = Nester(sequence, initial_threshold, threshold_multiplier, dependency_resolver, solo_ltrs)

        sketcher.create_gff(nester.nested_element, dirpath=output_folder, output_fasta_offset=output_fasta_offset, format=format)

        sketcher.create_gff(nester.nested_element, dirpath=output_folder, output_fasta_offset=output_fasta_offset, format=format)

        

        if solo_ltrs:

            sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)

            sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)

            

        sketcher.create_trf_gff(nester.trf, nester.seqid, dirpath=output_folder)

        sketcher.create_trf_gff(nester.trf, nester.seqid, dirpath=output_folder)

        if sketch:

        if sketch:

            if format != 'default':

            if format != 'default':

nested/core/nester.py

+7 −4
Original line number Original line Diff line number Diff line
@@ -21,7 +21,7 @@ class Nester(ToolInterface): 
        nested_element (NestedElement): nested element

        nested_element (NestedElement): nested element

    """

    """





    def __init__(self, sequence, threshold, multiplier, dependency_resolver):

    def __init__(self, sequence, threshold, multiplier, dependency_resolver, solo):

        self.seqid = sequence.id

        self.seqid = sequence.id

        self.sequence = sequence.seq

        self.sequence = sequence.seq

        self.nested_element = None

        self.nested_element = None
@@ -32,6 +32,7 @@ class Nester(ToolInterface): 
        self.multiplier = multiplier

        self.multiplier = multiplier

        self.dependency_resolver = dependency_resolver

        self.dependency_resolver = dependency_resolver

        self.trf = []

        self.trf = []

        self.solo = solo

        self._find_nesting()

        self._find_nesting()





    def _find_nesting(self):

    def _find_nesting(self):
@@ -56,9 +57,11 @@ class Nester(ToolInterface): 
        if not candidates:

        if not candidates:

            best_candidate = gene.get_best_candidate()

            best_candidate = gene.get_best_candidate()

            if not best_candidate:

            if not best_candidate:

                if solo:

                    self.solo_ltrs.find_solo_ltrs(sequence)

                    self.solo_ltrs.find_solo_ltrs(sequence)

                    self.solo_ltrs.solo_ltrs.sort(key=lambda x: x.location[0], reverse=True)

                    self.solo_ltrs.solo_ltrs.sort(key=lambda x: x.location[0], reverse=True)

                    return self.solo_ltrs.solo_ltrs

                    return self.solo_ltrs.solo_ltrs

                return []

            candidates = [best_candidate]

            candidates = [best_candidate]





        # sort by score (from highest)

        # sort by score (from highest)