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jamesamcl / pysbolgraph

Simple native Python library to read and write Synthetic Biology Open Language (SBOL) files 🐍
http://sbolstandard.org
BSD 2-Clause "Simplified" License
5 stars 5 forks source link

Add support to read and write GenBank files #4

Open jamesamcl opened 5 years ago

jamesamcl commented 5 years ago

Interoperability with BioPython may be the easiest way to enable this.

vsomnath commented 5 years ago

Hi James, Finally getting around to working on this, with my exams completed.

I was reading the SBOL specification manual and found this paragraph on GenericTopLevel.

Custom data can also be embedded at the top level of an SBOL document. The GenericTopLevel class is used to represent top-level entities whose purpose is to contain a set of annotations that are independent of any other class of SBOL object. Entities that have independent existence and are not recognized by the SBOL standard are deserialized to GenericTopLevel objects. These GenericTopLevel objects can be safely used by tools to exchange non-SBOL data.

Does the data from GenBank & similarly FASTA files go into this container?

jamesamcl commented 5 years ago

Ideally a GenBank file would be converted into objects in the SBOL2 data model, such as ComponentDefinition, Sequence, SequenceAnnotation, etc.