SBOL-utilities

SBOL-utilities is a collection of scripts and functions for manipulating SBOL 3 data that can be run from the command line or as functions in Python.

Installation

SBOL utilities requires Python 3.7+.

To install the package and all dependences, run:

pip3 install sbol-utilities

Certain utilities also have non-Python dependencies, which must be installed separately:

• graph-sbol requires Graphviz to be able to render diagrams.
• sbol-converter requires node.js to be able to locally run Javascript.

Utilities

Graph SBOL Documents

The graph_sbol utility uses graphviz to render the object tree in an sbol Document. In addition it will write PDF and Graphviz source files.

To use in context of an application:

import sbol3
from sbol_utilities.graph_sbol import graph_sbol

doc = sbol3.Document()
doc.read('my_file.ttl')
graph_sbol(doc)

To run as a commandline executable:

graph-sbol -i my_file.ttl

Convert an Excel template file to SBOL

The excel-to-sbol utility reads an Excel file specifying a library of basic and composite parts, formatted following sbol_library_template.xlsx.

Convert beween SBOL3 and other genetic design formats

The sbol-converter utility converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats.

Additional "macro" utilities convert specifically between SBOL3 and one of the other formats:

• sbol2fasta and fasta2sbol convert from SBOL3 to FASTA and vice versa
• sbol2genbank and genbank2sbol convert from SBOL3 to GenBank and vice versa
• sbol3to2 and sbol2to3 convert to and from SBOL2

Expand the combinatorial derivations in an SBOL file

The sbol-expand-derivations utility searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.

Calculate sequences of DNA components in an SBOL file

The sbol-calculate-sequences utility attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.

Compute the difference between two SBOL3 documents

The sbol-diff utility computes the difference between two SBOL3 documents and reports the differences.