Goodbye-Genbank

About Goodbye, GenBank

Goodbye, GenBank converts SeqFeature sequence annotations from NCBI GenBank records to a common and simplified format. GenBank feature annotations have a feature key and reasonably well defined qualifiers, but non-standard and discontinued feature types and qualifiers are commonly used and often the feature key is something someone made up and not a valid GenBank feature key. And even when a valid GenBank feature key is used, it is often incomplete and useless without additional details in the qualifiers.

This package converts most feature keys to appropriate Sequence Ontology terms used by GFF3 and SBOL. Non-standard qualifiers are repaired or removed.

Goodbye, GenBank is intended for those who wish to clean-up their GenBank files and then transition to a different format. The philosophy of this project is to salvage what is salvageable and to discard what is not. GenBank feature types are translated to Sequence Ontology terms; qualifiers are converted into a reduced set that contains only the parts that are not broken. Qualifiers are also converted to their correct type: int for integers, list only for qualifiers that can appear multiple times, bool for flags.

Moreover, different options are available to configure what is kept and what is thrown away.

Installation

pip install gbgb

Example

>>> feature
SeqFeature(FeatureLocation(ExactPosition(2931), ExactPosition(2936), strand=1), type='-10_signal')
>>> feature.qualifiers
{'ApEinfo_fwdcolor': ['pink'],
 'ApEinfo_graphicformat': ['arrow_data {{0 1 2 0 0 -1} {} 0} width 5 offset 0'],
 'ApEinfo_revcolor': ['pink'],
 'label': ['RNAII Promoter (-10 signal)']}
>>>
>>> from gbgb import convert_feature
>>> feature = convert_feature(feature)
>>> feature
SeqFeature(FeatureLocation(ExactPosition(2931), ExactPosition(2936), strand=1), type='minus_10_signal')
>>> feature.qualifiers
{'note': 'RNAII Promoter (-10 signal)'}
>>>
>>> from gbgb import genbank_feature_key
>>> genbank_feature_key('minus_10_signal')
'regulatory'

Documentation

gbgb

• convert_feature_type(feature: Bio.SeqFeature) -> str

  Finds a Sequence Ontology term for a GenBank feature.

  This function requires a :class:SeqFeature as opposed to just a GenBank feature key, since the type of a GenBank feature is not always fully described by its feature key. For example a regulatory GenBank feature could have a /regulatory_class="promoter" qualifier.

  Returns a Sequence Ontology term for the type of this feature

• convert_feature(feature: Bio.SeqFeature, qualifiers=gbgb.maps.qualifiers.DEFAULT_QUALIFIER_TRANSFORMERS) -> Bio.SeqFeature

  Returns a Bio.SeqFeature with valid GenBank qualifiers and a feature type that is a Sequence Ontology term.

• unconvert_feature(feature: Bio.SeqFeature) -> Bio.SeqFeature

  Restores a feature to its sad former shape.

  To "clean up" a GenBank feature while maintaining it's format, use unconvert_feature(convert_feature(feature)).

  Returns a SeqFeature with each qualifier being a list and having a GenBank feature key

• genbank_feature_key(sequence_feature_term: str, idempotent=True) -> str

  Returns a GenBank feature key for the provided Sequence Ontology term

gbgb.maps.qualifiers

The following are transformation functions. They take two identical qualifiers objects, before and after and update after to reflect the updated qualifiers. All of these functions return after.

• remove_protein_id_and_add_to_xrefs(before: dict, after: dict) -> dict

  Protein IDs are codes such as "AAF19666.1", which come from "International collaborators" and should all be on GenBank. This translation function removes the /protein_id="" qualifier and instead adds a /db_xref="" qualifier.

  Removes any malformed protein IDs as they are useless.

• rename_label_to_note(before: dict, after: dict) -> dict

  The /label="" qualifier was discontinued in 2010, but is still used frequently.

  See GenBank Release 180.

• GENBANK_SINGLE_QUALIFIERS: [str]

• format_single_qualifiers(before: dict, after: dict) -> dict

• GENBANK_INTEGER_QUALIFIERS: [str]

• format_integer_qualifiers(before: dict, after: dict) -> dict

• GENBANK_FLAG_QUALIFIERS: [str]

• format_flag_qualifiers(before: dict, after: dict) -> dict

• APE_QUALIFIER_NAMESPACE = 'ApEinfo_'

• remove_ape_a_plasmid_editor_qualifiers(before: dict, after: dict) -> dict

• GENE_RELATED_FEATURES: [str]

• GENBANK_QUALIFIER_FEATURE_KEYS: {str: [str]}

• GENBANK_QUALIFIERS: [str]

• remove_unrecognized_qualifiers(before: dict, after: dict) -> dict

The transformation function has one additional argument:

• remove_qualifiers_inappropriate_for_feature(before: dict, after: dict, genbank_feature_key: str) -> dict

  Removes all qualifiers that are not valid for a certain genbank feature key.

• DEFAULT_QUALIFIER_TRANSFORMERS: [callable]

  DEFAULT_QUALIFIER_TRANSFORMERS = (
      format_single_qualifiers,
      format_integer_qualifiers,
      format_flag_qualifiers,
      remove_protein_id_and_add_to_xrefs,
      rename_label_to_note,
      remove_unrecognized_qualifiers,
  )
  

gbgb.maps.features

• DEFAULT_SO_TERM = 'sequence_feature'

• GENBANK_DISCONTINUED_FEATURE_KEY_SO_TERMS: {str: str}

• GENBANK_FEATURE_KEY_SO_TERMS: {str: str}

• SO_TERM_GENBANK_FEATURE_KEYS: {str: str}

• GENBANK_FEATURE_KEYS: [str]

• UNAMBIGUOUS_INVALID_KEY_SO_TERMS: {str: str}

• GENBANK_REGULATORY_DEFAULT_SO_TERM = 'regulatory_region'

• GENBANK_REGULATORY_CLASS_SO_TERMS: {str: str}

• GENBANK_NC_RNA_DEFAULT_SO_TERM = 'ncRNA_gene'

• GENBANK_NC_RNA_CLASS_SO_TERMS: {str: str}

• GENBANK_MOBILE_ELEMENT_DEFAULT_SO_TERM: 'mobile_genetic_element'

• GENBANK_MOBILE_ELEMENT_TYPE_SO_TERMS: {str: str}

• GENBANK_REPEAT_REGION_DEFAULT_SO_TERM = 'repeat_region'

• GENBANK_REPEAT_TYPE_SO_TERMS: {str: str}

• GENBANK_PSEUDOGENE_DEFAULT_SO_TERM = 'pseudogene'

• GENBANK_PSEUDOGENE_TYPE_SO_TERMS: {str: str}

• DEFAULT_GENBANK_FEATURE_KEY = 'misc_feature'

gbgb.utils

• single(qualifiers: dict, name: str, on_multiple_ignore=False: bool)

  Converts qualifiers[name] from a list-like object to a single item. If on_multiple_ignore is True, skips qualifiers that are defined multiple times; otherwise, returns the first qualifier. If qualifiers[name] is not list-like, returns it.

  Returns a single value for the qualifier; None if the qualifier has no value.

• as_set(qualifiers) -> set

• as_list(qualifiers) -> list

Design considerations

For the most part, Goodbye, GenBank attempts to be idempotent, i.e. features and their types/keys and qualifiers can be safely transformed any number times with the same settings. The apparent mismatch between the conversion to Sequence Ontology feature terms and valid/fixed GenBank qualifiers is to simplify downstream processing. It is up to the users which qualifiers they wish to keep, but at least the choices they are given are reasonable.

Authors and Contributors

Goodbye, Genbank is written and maintained by Lars Schöning (@lyschoening).

Support or Contact

If you have any questions or suggestions or if you have found a unique new specimen of GenBank files that you would like to convert, please open an issue.