def annotate_samples_table(self, input, sample_expr, root=None, code=None, config=None): """Annotate samples with delimited text file (text table). :param str input: Path to delimited text file. :param str sample_expr: Expression for sample id (key). :param str root: Sample annotation path to store text table. :param str code: Annotation expression. :param config: Configuration options for importing text files :type config: :class:`.TextTableConfig` or None """ pargs = ['annotatesamples', 'table', '-i', input, '--sample-expr', sample_expr] if root: pargs.append('--root') pargs.append(root) if code: pargs.append('--code') pargs.append(code) if not config: config = TextTableConfig() pargs.extend(config.as_pargs()) return self.hc.run_command(self, pargs)
def import_annotations_table(self, path, variant_expr, code=None, npartitions=None, config=None): """Import variants and variant annotations from a delimited text file (text table) as a sites-only VariantDataset. :param path: The files to import. :type path: str or list of str :param str variant_expr: Expression to construct a variant from a row of the text table. Must have type Variant. :param code: Expression to build the variant annotations. :type code: str or None :param npartitions: Number of partitions. :type npartitions: int or None :param config: Configuration options for importing text files :type config: :class:`.TextTableConfig` or None :rtype: :class:`.VariantDataset` """ pargs = ['importannotations', 'table'] if isinstance(path, str): pargs.append(path) else: for p in path: pargs.append(p) pargs.append('--variant-expr') pargs.append(variant_expr) if code: pargs.append('--code') pargs.append(code) if npartitions: pargs.append('--npartition') pargs.append(npartitions) if not config: config = TextTableConfig() pargs.extend(config.as_pargs()) return self.run_command(None, pargs)
def annotate_global_table(self, input, root, config=None): """Load delimited text file (text table) into global annotations as Array[Struct]. :param str input: Input text file. :param str root: Global annotation path to store text table. :param config: Configuration options for importing text files :type config: :class:`.TextTableConfig` or None """ pargs = ['annotateglobal', 'table', '-i', input, '-r', root] if not config: config = TextTableConfig() pargs.extend(config.as_pargs()) return self.hc.run_command(self, pargs)
def annotate_variants_table(self, path, variant_expr, root=None, code=None, config=None): """Annotate variant with delimited text file (text table). :param path: Path to delimited text files. :type path: str or list of str :param str variant_expr: Expression for Variant (key). :param str root: Variant annotation path to store text table. :param str code: Annotation expression. :param config: Configuration options for importing text files :type config: :class:`.TextTableConfig` or None """ pargs = ['annotatevariants', 'table', '--variant-expr', variant_expr] if root: pargs.append('--root') pargs.append(root) if code: pargs.append('--code') pargs.append(code) if not config: config = TextTableConfig() pargs.extend(config.as_pargs()) if isinstance(path, str): pargs.append(path) else: for p in path: pargs.append(p) return self.hc.run_command(self, pargs)
def annotate_variants_loci(self, path, locus_expr, root=None, code=None, config=None): """Annotate variants from an delimited text file (text table) indexed by loci. :param str path: Path to delimited text file. :param str locus_expr: Expression for locus (key). :param str root: Variant annotation path to store annotation. :param str code: Annotation expression. :param config: Configuration options for importing text files :type config: :class:`.TextTableConfig` or None """ pargs = ['annotatevariants', 'loci', '--locus-expr', locus_expr] if root: pargs.append('--root') pargs.append(root) if code: pargs.append('--code') pargs.append(code) if not config: config = TextTableConfig() pargs.extend(config.as_pargs()) if isinstance(path, str): pargs.append(path) else: for p in path: pargs.append(p) return self.hc.run_command(self, pargs)