Commit 9328f294 authored by Ivan Vanat's avatar Ivan Vanat
Browse files

modules: fixed sketcher; fixed bug in output generators

parent 4e77d509

nested/cli/nester.py

+3 −3
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ import glob 
from concurrent import futures

from datetime import datetime

from subprocess import CalledProcessError

from typing import NoReturn, Optional, Any

from typing import NoReturn, Optional, Any, List



from Bio import SeqIO

from Bio.Seq import Seq
@@ -73,7 +73,7 @@ def main(input_fasta: str, sketch: bool, format: str, output_fasta_offset: int, 


def process_sequence(sequence: Seq, sketcher, sketch: bool, format: str,

                     output_fasta_offset: int, output_folder: str, initial_threshold: int,

                     threshold_multiplier: float, errors: int,

                     threshold_multiplier: float, errors: List[int],

                     dependency_resolver: DependencyResolver) -> NoReturn:

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

    seq_start_time = datetime.now()
@@ -85,7 +85,7 @@ def process_sequence(sequence: Seq, sketcher, sketch: bool, format: str, 
    output = [NesterOutputGenerator(output_folder, output_fasta_offset)]



    if sketch:

        output.append(NesterSketcherOutputGenerator(output_folder))

        output.append(NesterSketcherOutputGenerator(output_folder, output_fasta_offset))



    type = TE

    module_nester = Module("nester", nester, type, output)

nested/core/tools/ltr/te_finder.py

+2 −4
Original line number Diff line number Diff line
@@ -40,7 +40,6 @@ class TeFinder(DiscoveryToolInterface): 
                        tmp_file,

                        'fasta')



        print("STARTING LTR FINDER")

        # call LTR finder and feed stdin to it

        process = subprocess.Popen(

            [config['ltr']['path']] + args_dict_to_list(config['ltr']['args']) + [
@@ -51,8 +50,7 @@ class TeFinder(DiscoveryToolInterface): 
        # os.remove('/tmp/nested/ltr/{}.fa'.format(seqid))



        stdout, stderr = process.communicate()

        print("FINISHED LTR FINDER")

        print(stdout)



        parsed_output = self._parse_raw_output(stdout)

        for entry in parsed_output:

            params = {
@@ -78,7 +76,7 @@ class TeFinder(DiscoveryToolInterface): 
            dict: parsed raw output

        """

        entries = raw_output.decode('utf-8').split('>Sequence: ')

        print(raw_output.decode('utf-8'))



        for e in entries:

            entry_name = e.split(' ')[0]

            if entry_name == 'Program':

nested/core/tools/nester.py

+0 −4
Original line number Diff line number Diff line
@@ -55,10 +55,6 @@ class Nester(ToolInterface): 
                return []

            candidates = [best_candidate]



        print(f"iteration {self._iteration}")

        for c in candidates:

            print(c)



        # sort by score (from highest)

        candidates.sort(key=lambda x: x.score, reverse=True)

        # remove intersections

nested/core/tools/tandem_repeat_finder.py

+3 −7
Original line number Diff line number Diff line
@@ -44,12 +44,10 @@ class TandemRepeatFinder(ToolInterface): 


        repeats = self._filter_candidates(self._get_candidates(self.seqId))

        repeats.sort(key=lambda repeat: repeat.location[0], reverse=True)

        print("CHOSEN")

        for r in repeats:

            print(r)



        self.output_object = TrfOutputObject(self.seqId, sequence, repeats)



        #self.cleanup()

        self.cleanup()



        return repeats
@@ -62,9 +60,7 @@ class TandemRepeatFinder(ToolInterface): 
                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]))

        print("CANDIDATES")

        for c in candidates:

            print(c)



        return candidates



    def _filter_candidates(self, candidates: List[TandemRepeat]) -> List[TandemRepeat]:

nested/output/output_generators/base_output_generator.py

+6 −2
Original line number Diff line number Diff line 
#!/usr/bin/env python3

import os

from typing import Type, NoReturn

from typing import NoReturn



from nested.output.output_objects.base_output_object import BaseOutputObject
@@ -11,5 +11,9 @@ class BaseOutputGenerator: 
    def __init__(self, directory: str):

        self.directory = os.path.join(directory, self.default_directory)



    def generate_output(self, output_object: Type[BaseOutputObject]) -> NoReturn:

    def generate_output(self, output_object: BaseOutputObject) -> NoReturn:

        pass



    def create_data_directory(self, sequence_id: str) -> NoReturn:

        if not os.path.exists('{}/{}'.format(self.directory, sequence_id)):

            os.makedirs('{}/{}'.format(self.directory, sequence_id))