global-biofoundries-alliance / synbiopython Goto Github PK

General low-level API

License: MIT License

Python 100.00%

synbiopython's Introduction

SynBioPython

SynBiopython provides generic tools for Synthetic Biology. For more details, please see the publication:

SynBiopython: an open-source software library for Synthetic Biology, Jing Wui Yeoh, Neil Swainston, Peter Vegh, Valentin Zulkower, Pablo Carbonell, Maciej B Holowko, Gopal Peddinti, Chueh Loo Poh. Synthetic Biology (2021) ysab001

Installation

pip install synbiopython

To install the latest version from Github:

pip install git+https://github.com/Global-Biofoundries-Alliance/SynBioPython

Currently Python 3.6, 3.7 and 3.8 are supported.

Usage

You should now be able to run this in Python:

import synbiopython
print(synbiopython.__version__)

Currently, there are three modules implemented:

The genbabel module provides standard file parsers and for working with multiple fileformats.
The codon module provides support for codon optimisation.
The lab automation module enables working with plates and generation of picklists (transfers) for liquid handlers.

Examples

Example Jupyter notebooks are provided for each module: codon, genbabel and lab automation. In order to open these notebooks, download and install JupyterLab.

Contribute!

SynBiopython is developed collectively by members of the Global Biofoundry Alliance and released on Github under the MIT license. Contributions are welcome!

synbiopython's People

Contributors

Stargazers

Watchers

Forkers

edinburgh-genome-foundry frba concordiagenomefoundry gopalpeddinti yeohjingwui sandracastillopriego jingwui mholowko ashuein chengzyn ianderrington j1souza hiyama341 00mjk siatliu babak-bashirzadeh nulllabtests

synbiopython's Issues

Formatter preferences (Flake8, Black, etc.)

Would be nice to enforce formatting using e.g. Black (which seems to be very popular). I'm think there are some ways to check/correct PEP8 and other formatting errors at commit time but I've never done it.

How do we feel about dependencies?

Few dependencies is a nice trait in a library. Biopython's only dependency seems to be Numpy.

I am asking because Plateo depends on a few heavy libraries (the core can be standalone, but dealing with spreadsheets is easier with Pandas/xlrd), and I expect other modules may depend on at least Biopython and a few others.

using type hint/type annotation by default

Type hinting has been revamped in python 3.5 (I think), and offers a consistent notation for type hinting in the source code:
http://veekaybee.github.io/2019/07/08/python-type-hints/

Most IDEs now support this, and checks the type hints during coding, also packages can do type checking before commiting to the repo. I highly recommend it!

Any questions, comments?

Testing environment preferences for SynBioPython

The EGF software relies on pytest / TravisCI / coveralls for testing. Any other suggestions?

Use of Pylint?

As discussed, I'd suggest that we add Pylint to the list of tools that we validate our code against before check-in:

https://www.pylint.org/

Pylint integrates with most IDEs and can be made to run automatically and flag up both formatting errors but also (importantly) potentially bugs. It's very powerful and can catch issues with very little effort from the user.

Please reply to this thread, even with "OK" if you're fine with this, or please disagree if you'd like!

No module named synbiopython.genbabel found when importing synbiopython on Colab Notebook

Hi, I'm trying to learn to use SynBioPython with Google Colab python notebooks. I'm able to pip install synbiopython and import synbiopython with Colab notebooks, but when I try to import synbiopython.genbabel as stdgen, it throws this error:

Synbiopython on PyPI

Hi everyone - I went ahead and pushed the synbiopython projet on PyPI to reserve the name:

https://pypi.org/project/synbiopython/0.0.1/

It would be nice if the PyPI package's ownership was shared between accounts from different froundries to ensure every team can easily update the repo if necessary (right now it's only EdinburghGenomeFoundry). Let us know your PyPI username and we'll add you.

synbiopython.org redirects to a malware site

The advertised url for this software, synbiopython.org, is currently redirecting to what appears to be a malware site.

Either the maintainers need to reclaim the URL or else they should remove it and warn users.