Module: ncbi.datasets.metadata.genome
Utility functions for working and reporting on assembly data descriptors.
Module: ncbi.datasets.metadata.genome
- ncbi.datasets.metadata.genome.print_assembly_warning_or_error(assembly_match: ncbi.datasets.openapi.model.v1_assembly_match.V1AssemblyMatch)
Reports assembly warnings and/or errors per query term
- Parameters
assembly_match – A single assembly metadata record returned by the API
- Returns
None
- Side Effects:
Prints report to stdout.
- ncbi.datasets.metadata.genome.assembly_values_by_fields(assembly: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptor.V1AssemblyDatasetDescriptor, fields=typing.List[str])
Filters assembly descriptor for provided fields
- Parameters
assembly_descriptor – A single assembly descriptor record returned by the API
fields – List of top-level fields to allow into returned dict
- Returns
dict of supplied fields to their values
- Side Effects:
Prints report to stdout.
- ncbi.datasets.metadata.genome.print_assembly_metadata_by_fields(assembly_match: ncbi.datasets.openapi.model.v1_assembly_match.V1AssemblyMatch, fields=typing.List[str])
Reports selected fields for a V1AssemblyMatch object to stdout
Warning/Error code will be printed if the supplied assembly object does not contain a assembly field.
- Parameters
assembly_match – A single assembly metadata record returned by the API
fields – A list of top-level field names to display. If set to None, print the entire object.
- Returns
None
- Side Effects:
Prints report to stdout.
- ncbi.datasets.metadata.genome.get_assembly_metadata_by_taxon(taxon: Union[str, int], **kwargs)
Return iterable assembly metadata for a taxon
Warning/Error code will be printed if the supplied taxon has no assembly.
- Parameters
taxon –
- Returns
iterable assemblies
- Side Effects:
Prints error to stdout.
- ncbi.datasets.metadata.genome.get_assembly_metadata_by_asm_accessions(genome_assembly_accessions: List[str], **kwargs)
Return iterable assembly metadata for a list of assembly accessions
Warning/Error code will be printed if the supplied accessions are invalid.
- Parameters
genome_assembly_accessions – A list of NCBI assembly accessions
- Returns
iterable assemblies
- Side Effects:
Prints error to stdout.
- ncbi.datasets.metadata.genome.get_assembly_metadata_by_bioproject_accessions(bioproject_accessions: List[str], **kwargs)
Return iterable assembly metadata for a list of BioProject accessions
Warning/Error code will be printed if the supplied BioProject has no assembly.
- Parameters
bioproject_accessions – A list of NCBI bioproject accessions
- Returns
iterable assemblies
- Side Effects:
Prints error to stdout.
- ncbi.datasets.metadata.genome.iterate_reply(genome_api_func, func_arg, **kwargs)