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. Additional documentation is online at readthedocs.io.

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:

sbol-to-fasta and fasta-to-sbol convert from SBOL3 to FASTA and vice versa
sbol-to-genbank and genbank-to-sbol convert from SBOL3 to GenBank and vice versa
sbol3-to-sbol2 and sbol2-to-sbol3 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.

Contributing

We welcome contributions that patch bugs, improve existing utilities or documentation, or add new utilities! For guidance on how to contribute effectively to this project, see CONTRIBUTING.md.