How to use generate_variant_id method in avocado

Best Python code snippet using avocado_python

vcfgraph.py

Source:vcfgraph.py

...54            "Reference intervals:", pformat(list(self.get_ref_alleles()))55        ]56        return "\n".join(s)57    @staticmethod58    def generate_variant_id(record, varIdCounts=None):59        """60        Generate a variant ID for a pySAM VCF record61        :param record: a pysam record62        :param varIdCounts: defaultdict dictionary of counts per variant ID:63                            varIdCounts = defaultdict(int)64        :return: variant ID string65        """66        if record.id:67            varId = record.id68            if varIdCounts is not None:69                if varId in varIdCounts:70                    raise Exception("Duplicated variant ID: {}".format(varId))71                varIdCounts[varId] = 172        else:73            varId = "{}:{}".format(record.chrom, record.pos)74            if varIdCounts is not None:75                varIdCounts[varId] += 176                varId = "{}-{}".format(varId, varIdCounts[varId])77        return varId78    @staticmethod79    def generate_allele_ids(record, varId):80        return [("{}:{}".format(varId, n), record.alleles[n]) for n in range(len(record.alleles))]81    @staticmethod82    def create_from_vcf(ref_file_name,83                        vcf_file_name,84                        ins_info_key,85                        chrom=None, start=None, end=None,86                        padding_length=150,87                        allele_graph=False):88        """ Create a VCFGraph object from a VCF input file89        :param ref_file_name: Reference Fasta name90        :param vcf_file_name: VCF file name91        :param chrom: chromosome to read from92        :param start: start position for tabix / VCF fetch93        :param end: end position for tabix / VCF fetch94        :param padding_length: length of reference padding95        :param allele_graph: Create an allele graph, rather than haplotype graph96        :return: a VCFGraph97        """98        vcf = pysam.VariantFile(vcf_file_name)99        graph = VCFGraph(ref_file_name, chrom)100        varIdCounts = defaultdict(int)101        record_count = 0102        for record in vcf.fetch(chrom, start, end):103            logging.debug("Processing: %s", str(record).rstrip())104            if chrom is None:105                chrom = record.chrom106                graph.chrom = chrom107            elif chrom != record.chrom:108                break109            if graph.first_pos is None:110                graph.first_pos = record.pos111            if graph.last_pos is None or graph.last_pos < record.stop:112                graph.last_pos = record.stop113            varId = VCFGraph.generate_variant_id(record, varIdCounts)114            record_count += 1115            graph.add_record(record, allele_graph, varId, ins_info_key)116        if not record_count:117            raise NoVCFRecordsException("No VCF records found at {}:{}-{}".format(chrom, start, end))118        graph.add_ref_support(graph.first_pos - padding_length, graph.last_pos + padding_length)119        # Split read nodes for ALTs to link into (esp. for remote breakends)120        for be in graph.alts.values():121            if graph.first_pos <= be.end <= graph.last_pos:122                graph.refs.slice(be.end + 1)123            else:124                graph.add_ref_support(be.end + 1, be.end + padding_length)125        return graph126    def add_record(self, vcf, allele_graph, varId, ins_info_key):127        """ Add one vcfRecord to the graph...

varianter.py

Source:varianter.py

...29    :param variant: Avocado test variant (list of TreeNode-like objects)30    :return: True when the variant does not contain (any useful) data31    """32    return not variant or variant == [tree.TreeNode()] * len(variant)33def generate_variant_id(variant):34    """35    Basic function to generate variant-id from a variant36    :param variant: Avocado test variant (list of TreeNode-like objects)37    :return: String compounded of ordered node names and a hash of all38             values.39    """40    def get_variant_name(variant):41        """42        To get the variant full name string43        :param variant: Avocado test variant (list of TreeNode-like objects)44        :return: Complete variant name string45        """46        full_name = []47        for node in variant:...

burden_test.py

Source:burden_test.py

...32        for k, v in opencga_d.items():33            values = "\t".join([i for i in v])34            vid = k.replace("_", "\t")35            fout.write(f"{vid}\t{values}")36def generate_variant_id(*strings):37    """_summary_38    Returns:39        _type_: _description_40    """41    res = "_".join([str(i) for i in strings])42    return res43def get_vid_opencga(file: str, generate_vid=False) -> set:44    """_summary_45    Args:46        file (str): _description_47    Returns:48        set: _description_49    """50    df = pd.read_csv(file, sep="\t")51    if generate_variant_id:52        df["vid"] = df.apply(53            lambda row: generate_variant_id(54                row["chr"], row["pos"], row["ref"], row["alt"]55            ),56            axis=1,57        )58    return {i for i in df["vid"].tolist()}59def biomart_to_burden(file_path: str, outpath: str) -> None:60    """_summary_61    Args:62        file_path (str): _description_63        outpath (str): _description_64    """65    with open(file_path, "r") as fhand:66        next(fhand)67        lines = [i.strip() for i in fhand.readlines()]...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.