How to use _valid_variant method in avocado

Best Python code snippet using avocado_python

utils.py

Source:utils.py

...274    else:275        query_cmd = 'virt-install --os-variant list'276    os_variants = run(query_cmd).stdout277    os_patterns = [r"rhel\d+.?\d*", r"win\d+[.k]?\d?[r]?2?"]278    def _valid_variant(variant):279        return bool(re.search(r"%s" % variant, os_variants, re.MULTILINE))280    def _replace_variant(variant):281        if variant.startswith("win"):282            var_dict = {'2000': '2k', '2003': '2k3', '2008': '2k8'}283            for key in var_dict:284                if key in variant:285                    return variant.replace(key, var_dict[key])286        return variant287    os_variant = None288    for pat in os_patterns:289        os_variant = re.search(pat, vm_name, re.I)290        if os_variant:291            break292    if os_variant is None:293        LOGGER.warning("Can't determine os variant from name: %s", vm_name)294        return 'none'295    os_variant = _replace_variant(os_variant.group().lower())296    if _valid_variant(os_variant):297        return os_variant298    else:299        if os_variant.startswith('rhel'):300            default_rhel = "rhel7"301            if _valid_variant(os_variant[:5]):302                return os_variant[:5]303            else:304                return default_rhel305        if os_variant.startswith('win'):306            default_win = "win7"307            return default_win308def clean_vm(vm_name, uri=None, host=None):309    """310    Clean up specific VM name311    """312    cmd = 'virsh'313    if uri is not None:314        cmd += ' -c %s' % uri315    destroy_cmd = cmd + " destroy"...

mux.py

Source:mux.py

...62        Iterates through variants and process the internal filters63        :yield valid variants64        """65        for variant in self.iter_variants():66            if self._valid_variant(variant):67                yield variant68    def iter_variants(self):69        """70        Iterates through variants without verifying the internal filters71        :yield all existing variants72        """73        pools = []74        for pool in self.pools:75            if isinstance(pool, list):76                # Don't process 2nd level filters in non-root pools77                pools.append(itertools.chain(*(_.iter_variants()78                                               for _ in pool)))79            else:80                pools.append([pool])81        variants = itertools.product(*pools)82        while True:83            try:84                yield list(itertools.chain(*next(variants)))85            except StopIteration:86                return87    @staticmethod88    def _valid_variant(variant):89        """90        Check the variant for validity of internal filters91        :return: whether the variant is valid or should be ignored/filtered92        """93        _filter_out = set()94        _filter_only = set()95        for node in variant:96            _filter_only.update(node.environment.filter_only)97            _filter_out.update(node.environment.filter_out)98        if not (_filter_only or _filter_out):99            return True100        filter_only = tuple(_filter_only)101        filter_out = tuple(_filter_out)102        filter_only_parents = [str(_).rsplit('/', 2)[0] + '/'...

features.py

Source:features.py

...16    easy translation to a BED-like file. This allows variants to be17    worked on via genomic arithmetic18    """19    @staticmethod20    def _valid_variant(var: str, mode: str='reference') -> None:21        if mode not in {'reference', 'alternate'}:22            mode: str = 'reference'23        valid_chars: Set[str] = set('ACGT')24        msg: str = 'The %s allele must contain only %s' % (mode, ','.join(valid_chars))25        if mode == 'alternate':26            valid_chars.update(',*')27        if not set(var.upper()).issubset(valid_chars):28            raise ValueError(msg)29    @staticmethod30    def default_id(chrom: str, position: int, ref: str, alt: str) -> str:31        """Create a default variant ID32        Args:33            chrom (str): Chromomosome or contig of the variant34            position (int): Position of the variant35            ref (str): Reference allele36            alt (str): Alternate alleles separated by commas37        Returns:38            str: The variant ID as '%(chrom)s_%(position)s_%(ref)s_%(alt)s'39        """40        Bpileup._valid_variant(var=ref, mode='reference')41        Bpileup._valid_variant(var=alt, mode='alternate')42        return "%(chr)s_%(pos)s_%(ref)s_%(alt)s" % {43            'chr': chrom,44            'pos': position,45            'ref': ref,46            'alt': alt47        }48    @classmethod49    def frominterval(cls, interval: pybedtools.cbedtools.Interval) -> 'Bpileup':50        """Create a Bpileup from an Interval"""51        if interval.file_type != 'bed':52            raise TypeError("Must be a BED interval")53        elif len(interval.fields) != 6:54            raise ValueError("wrong number of fields")55        return cls(56            chrom=interval.chrom,57            position=interval.end,58            ref=interval.fields[4],59            alt=interval.fields[5],60            name=interval.fields[3]61        )62    def __init__(self, chrom: str, position: int, ref: str, alt: str, name: Optional[str]=None) -> None:63        """Initialize a Bpileup object64        Args:65            chrom (str): Chromosome/contig of the variant66            position (int): Position of the variant67            ref (str): Refererence allele of the variant68            alt (str): Alternate alleles in a comma-separated string69            name (str): Optional variant ID; if not provided, generated by Bpileup.default_id70        """71        #   Validate data72        ref: str = str(ref)73        alt: str = str(alt)74        self._valid_variant(var=ref, mode='reference')75        self._valid_variant(var=alt, mode='alternate')76        #   Fill in the data77        self._chrom: str = str(chrom)78        self._pos: int = int(position)79        self._ref: str = ref80        self._alt: Tuple[str, ...] = tuple(alt.split(','))81        if name:82            self._id: str = str(name)83        else:84            self._id: str = self._default_id()85    def __str__(self) -> str:86        out: Tuple = (87            self.chrom,88            self.dummy,89            self.position,...

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