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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()]...

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