We are working on a project to provide support for conversion between GenBank and SBOL3 (pysbol3) formats as part of Google Summer of Code 22. For many GenBank files, we repeatedly encounter "Features" for a record which are for locations with no fixed starting/ending point. These are referred to as "fuzzy" endpoints by BioPython; i.e
FeatureLocation objects can have start positions being "ExactPositions" or "BeforePositions" (meaning the particular feature is relevant for all base locations before and till a given location). Similarly, the end positions can be "ExactPositions" or "AfterPositions" (meaning the feature is relevant for all base locations after and from the given location).
SBOL3 currently only supports exact location endpoints which may lead to information loss/misinterpretation during conversions to and from GenBank.
Some new properties for the Range object would be ideal to resolve this, wherein they may store the information of the location endpoint being an exact one or a fuzzy one.
We are working on a project to provide support for conversion between GenBank and SBOL3 (pysbol3) formats as part of Google Summer of Code 22. For many GenBank files, we repeatedly encounter "Features" for a record which are for locations with no fixed starting/ending point. These are referred to as "fuzzy" endpoints by BioPython; i.e FeatureLocation objects can have start positions being "ExactPositions" or "BeforePositions" (meaning the particular feature is relevant for all base locations before and till a given location). Similarly, the end positions can be "ExactPositions" or "AfterPositions" (meaning the feature is relevant for all base locations after and from the given location).
SBOL3 currently only supports exact location endpoints which may lead to information loss/misinterpretation during conversions to and from GenBank. Some new properties for the Range object would be ideal to resolve this, wherein they may store the information of the location endpoint being an exact one or a fuzzy one.