Welcome to snekBOL’s documentation!

snekBOL is a python library for the reading and writing of Synthetic Biology Open Language (SBOL) 2.1.0 files. This is a Python 3 implementation of the standard and does not use a wrapper like pySBOL.

For more details on the SBOL standard see the official site.

Introduction

snekBOL is a python implementation of the Synthetic Biology Open Language (SBOL) standard. The current version of snekBOL is a very early version that aims to eventually fully support the 2.1.0 standard.

Installation

snekBOL supports Python 3 (tested on python 3.4+). It is almost pure python so should work on any OS that supports the libxml2 and libxlst libraries (required for lxml). It has been tested on MacOS and Linux; Windows may or may not be supported, I havn’t tested it.

Using pip

snekBOL can easily be installed from PyPi using pip. You must ensure that libxml2 and libxslt are install first otherwise it won’t install.

pip install snekbol

Using setup.py

If you require the latest development version you can download from Github and install manually. Again, like with pip you will need to have libxml2 and libxslt installed first.

  1. Get the code from github git clone https://github.com/tjomas/snekbol
  2. Change to the directory and install using python setup.py install

API

Annotation

Collection

class snekbol.collection.Collection(identity, members=[], **kwargs)

Bases: snekbol.identified.TopLevel

Groups together a set of TopLevel objects that have something in common

Component defintion

Components

Document

Identified

class snekbol.identified.Identified(identity, name=None, was_derived_from=None, version=None, description=None, display_id=None, annotations=[])

Bases: object

Mixin to provide identity support to SBOL objects

class snekbol.identified.TopLevel(identity, **kwargs)

Bases: snekbol.identified.Identified

Mixin to indicate SBOL object is top level and should not be nested

Location

Model

Sequence

Namespaces

snekbol.namespaces.NS(namespace, tag)

Generate a namespaced tag for use in creation of an XML file

Types

Indices and tables