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How to use _get_variants method in avocado

Best Python code snippet using avocado_python

project_version.py

Source:project_version.py

...36        self.variants.change_track(track_id=track_id, new_track=new_track)37        self.compositions.change_track(track_id=track_id, new_track=new_track)38        notify(message=NotificationMessage.TRACK_CHANGED, track_id=track_id, new_track=new_track)39        return self40    def _get_variants(self, variant_id: UUID) -> Variants:41        if any(variant.id == variant_id for variant in self.variants):42            return self.variants43        for composition in self.compositions:44            if any(variant.id == variant_id for variant in composition.variants):45                return composition.variants46        raise NoDataFound(47            f"Cannot find variant id {variant_id} in project version {[variant.id for variant in self.variants]} "48            f"{[variant.id for composition in self.compositions for variant in composition.variants]}"49        )50    def get_next_variant(self, variant_id: UUID, repeat: bool, raise_on_last: bool = False) -> Optional[Variant]:51        variants = self._get_variants(variant_id=variant_id)52        if raise_on_last and self.is_last_variant(variant_id=variant_id, repeat=repeat):53            raise OutOfVariants(f"{variant_id} {variants}")54        return variants.get_next_variant(variant_id=variant_id, repeat=repeat)55    def is_last_variant(self, variant_id: UUID, repeat: bool) -> bool:56        variants = self._get_variants(variant_id=variant_id)57        return variants.is_last_variant(variant_id=variant_id, repeat=repeat)58    def get_variant(self, variant_id: UUID) -> Variant:59        variants = self._get_variants(variant_id=variant_id)60        return variants.get_variant(variant_id=variant_id)61    def _get_compiled_sequence(self, variant_id: UUID, track: Track, include_preset: bool = True) -> Sequence:62        variant = self.get_variant(variant_id=variant_id)63        version_id = variant.get_track_variant_item(track=track).version_id64        return track.get_version(identifier=version_id).get_sequence(include_preset=include_preset)65    def get_compiled_sequence(66        self, variant_id: UUID, single_track: Track = None, include_preset: bool = True, raise_not_found: bool = True67    ) -> Sequence:68        variant = self.get_variant(variant_id=variant_id)69        if single_track:70            tracks = [single_track]71        else:72            tracks = [track for track in self.tracks if track.id in variant.get_enabled_tracks_ids()]73        if raise_not_found and not tracks:74            raise NoItemSelected(f"No tracks selected in current variant {variant.name}")75        sequence = None76        if tracks:77            sequence = copy.deepcopy(78                self._get_compiled_sequence(variant_id=variant_id, track=tracks.pop(0), include_preset=include_preset)79            )80            for track in tracks:81                sequence += copy.deepcopy(82                    self._get_compiled_sequence(variant_id=variant_id, track=track, include_preset=include_preset)83                )84        return sequence85    def get_total_num_of_bars(self, variant_id: UUID) -> int:86        variant = self.get_variant(variant_id=variant_id)87        variants = self._get_variants(variant_id=variant_id)88        track = self.tracks.get_track(identifier=variant.get_first_track_id())89        if variant.type == VariantType.SINGLE:90            return self.get_compiled_sequence(variant_id=variant_id, single_track=track).num_of_bars()91        return sum(92            self.get_compiled_sequence(variant_id=variant.id, single_track=track).num_of_bars() for variant in variants93        )94    def add_single_variant(self, name: str, selected: bool, enable_all_tracks: bool) -> Variant:95        variant = Variant.from_tracks(96            name=name,97            type_=VariantType.SINGLE,98            tracks=self.tracks,99            selected=selected,100            enable_all_tracks=enable_all_tracks,101        )...

variant.py

Source:variant.py

...79            out["variantcaller"] = vc80    if f.find("-germline-") >= 0:81        out["germline"] = full_f82    return out83def _get_variants(data):84    """Retrieve variants from CWL and standard inputs for organizing variants.85    """86    active_vs = []87    if "variants" in data:88        variants = data["variants"]89        # CWL based list of variants90        if isinstance(variants, dict) and "samples" in variants:91            variants = variants["samples"]92        for v in variants:93            # CWL -- a single variant file94            if isinstance(v, six.string_types) and os.path.exists(v):95                active_vs.append(_add_filename_details(v))96            elif (isinstance(v, (list, tuple)) and len(v) > 0 and97                  isinstance(v[0], six.string_types) and os.path.exists(v[0])):98                for subv in v:99                    active_vs.append(_add_filename_details(subv))100            elif isinstance(v, dict):101                if v.get("vrn_file"):102                    active_vs.append(v)103                elif v.get("population"):104                    vrnfile = v.get("population").get("vcf")105                    active_vs.append(_add_filename_details(vrnfile))106                elif v.get("vcf"):107                    active_vs.append(_add_filename_details(v.get("vcf")))108    return active_vs109def get_active_vcinfo(data, use_ensemble=True):110    """Use first caller if ensemble is not active111    """112    active_vs = _get_variants(data)113    if len(active_vs) > 0:114        e_active_vs = []115        if use_ensemble:116            e_active_vs = [v for v in active_vs if v.get("variantcaller") == "ensemble"]117        if len(e_active_vs) == 0:118            e_active_vs = [v for v in active_vs if v.get("variantcaller") != "ensemble"]119        if len(e_active_vs) > 0:120            return e_active_vs[0]121def extract_germline_vcinfo(data, out_dir):122    """Extract germline VCFs from existing tumor inputs.123    """124    supported_germline = set(["vardict", "octopus", "freebayes"])125    if dd.get_phenotype(data) in ["tumor"]:126        for v in _get_variants(data):127            if v.get("variantcaller") in supported_germline:128                if v.get("germline"):129                    return v130                else:131                    d = utils.deepish_copy(data)132                    d["vrn_file"] = v["vrn_file"]133                    gd = germline.extract(d, [d], out_dir)134                    v["germline"] = gd["vrn_file_plus"]["germline"]135                    return v136def extract_population_vcinfo(data):137    """Extract population level VCFs138    """139    for v in _get_variants(data):140        if v.get("population"):...

solve.py

Source:solve.py

...62        the_one_ = int(self._bitmask.replace("X", "1"), 2)63        the_zero_ = int(self._bitmask.replace("X", "0"), 2)64        return (integer & the_one_) | the_zero_65class ComputerPart2(Computer):66    def _get_variants(self, addr_mask):67        if "X" in addr_mask:68            for r in ("0", "1"):69                yield from self._get_variants(addr_mask.replace("X", r, 1))70        else:71            yield addr_mask72    def _assign_value(self, command):73        if command.assign_value():74            transformed_memory_address = "{0:036b}".format(command.memory_address)75            transformed_memory_address_ = ""76            for index, letter in enumerate(self._bitmask):77                if letter == "1":78                    transformed_memory_address_ += "1"79                elif letter == "0":80                    transformed_memory_address_ += transformed_memory_address[index]81                else:82                    transformed_memory_address_ += "X"83            for memory_address in self._get_variants(transformed_memory_address_):84                self._memory[int(memory_address, 2)] = command.value85        else:86            pass87def main():88    input_data = get_input_data("advent_of_code_2020/day14/input.txt")89    commands = parse(input_data)90    computer = Computer()91    for command in commands:92        computer.execute_command(command)93    result_part1 = sum(94        computer.get_value(memory_address)95        for memory_address in computer.get_written_memory_addresses()96    )97    print(...

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