sbol_utilities.sbol3_genbank_conversion

Module Contents

Classes

GenBankSBOL3Converter

Main Converter class handling offline, direction conversion of files SBOL3 files to and from GenBank files
class GenBankSBOL3Converter

Main Converter class handling offline, direction conversion of files SBOL3 files to and from GenBank files

While instantiating an instance of the converter, required builders must be registered in order to accurately parse modified or new SBOL3 class objects

class ComponentGenBankExtension(identity: str, types: Optional[Union[str, Sequence[str]]], **kwargs)

Bases: sbol3.Component

Overrides the sbol3 Component class to include fields to directly read and write extraneous properties of GenBank not storable in any SBOL3 data field. :extends: sbol3.Component class

GENBANK_EXTRA_PROPERTY_NS = http://www.ncbi.nlm.nih.gov/genbank
class CustomReferenceProperty(type_uri=CUSTOM_REFERENCE_NS, identity=None)

Bases: sbol3.CustomIdentified

Serves to store information and annotations for ‘Reference’ objects in GenBank file to SBOL3 while parsing so that it may be retrieved back in a round trip :extends: sbol3.CustomIdentified class

CUSTOM_REFERENCE_NS = http://www.ncbi.nlm.nih.gov/genbank#GenbankReference
class CustomStructuredCommentProperty(type_uri=CUSTOM_STRUCTURED_COMMENT_NS, identity=None)

Bases: sbol3.CustomIdentified

Serves to store information and annotations for ‘Structured_Comment’ objects in GenBank file to SBOL3 while parsing so that it may be retrieved back in a round trip Complete reference available at: https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/ :extends: sbol3.CustomIdentified class

CUSTOM_STRUCTURED_COMMENT_NS = http://www.ncbi.nlm.nih.gov/genbank#GenbankStructuredComment
class FeatureGenBankExtension(locations: List[sbol3.Location] = None, **kwargs)

Bases: sbol3.SequenceFeature

Overrides the sbol3 SequenceFeature class to include fields to directly read and write qualifiers of GenBank features not storable in any SBOL3 data field. :extends: sbol3.SequenceFeature class

GENBANK_FEATURE_QUALIFIER_NS = http://www.ncbi.nlm.nih.gov/genbank#featureQualifier
class LocationGenBankExtension(sequence: sbol3.Sequence = sbol3.Sequence('autoCreatedSequence'), *, identity: str = None, type_uri: str = GENBANK_RANGE_NS, **kwargs)

Bases: sbol3.Location

Overrides the sbol3 Location class to include fields to store the start and end position types (AfterPosition / BeforePosition / ExactPosition). :extends: sbol3.Location class

GENBANK_RANGE_NS = http://www.ncbi.nlm.nih.gov/genbank#locationPosition
BIO_STRAND_FORWARD = 1
BIO_STRAND_REVERSE
COMP_ROLES
COMP_TYPES
DEFAULT_GB_SEQ_VERSION = 1
DEFAULT_GB_TERM = misc_feature
DEFAULT_SO_TERM = SO:0000110
GB2SO_MAPPINGS_CSV
GENBANK_LOCATION_POSITION
SBOL_LOCATION_POSITION
SEQUENCE_ENCODING
SO2GB_MAPPINGS_CSV
TEST_NAMESPACE = https://test.sbol3.genbank/
gb2so_map
so2gb_map
convert_genbank_to_sbol3(self, gb_file: str, sbol3_file: str = 'sbol3.nt', namespace: str = TEST_NAMESPACE, write: bool = False) → sbol3.Document

Convert a GenBank document on disk into an SBOL3 document The GenBank document is parsed using BioPython, and corresponding objects of SBOL3 document are created

Parameters

  • gb_file – path to read GenBank file from

  • sbol3_file – path to write SBOL3 file to, if write set to true

  • namespace – URIs of Components will be set to {namespace}/{genbank_id}, defaults to “https://test.sbol3.genbank/”

  • write – writes the generated sbol3 document in SORTED_NTRIPLES format to provided sbol3_file path

Returns

SBOL3 document containing converted materials

convert_sbol3_to_genbank(self, sbol3_file: str, doc: sbol3.Document = None, gb_file: str = 'genbank.out', write: bool = False) → Dict

Convert a SBOL3 document on disk into a GenBank document The GenBank document is made using an array of SeqRecords using BioPython, by parsing SBOL3 objects

Parameters

  • sbol3_file – path to read SBOL3 file from

  • gb_file – path to write GenBank file to, if write set to true

  • write – writes the generated genbank document to provided path

Returns

Array of SeqRecord objects which comprise the generated GenBank document

create_gb2so_role_mappings(self, gb2so_csv: str = GB2SO_MAPPINGS_CSV, so2gb_csv: str = SO2GB_MAPPINGS_CSV, convert_gb2so: bool = True, convert_so2gb: bool = True) → int

Reads 2 CSV Files containing mappings for converting between GenBank and SequenceOntology (SO) roles :param gb2so_csv: path to read genbank to so conversion csv file :param so2gb_csv: path to read so to genbank conversion csv file :param convert_gb2so: bool stating whether to read csv for genbank to SO mappings :param convert_so2gb: bool stating whether to read csv for SO to genbank mappings :return: int 1 / 0 denoting the status of whether the mappings were created and stored in dictionaries