rnajena-sugar 0.9.0

A Python framework for bioinformatics

A Python framework for bioinformatics

The sugar project aims to provide a lightweight framework to facilitate rapid application development for bioinformatics.

It thus provides classes and functions for working with DNA and RNA sequences, as well as related annotations, and it provides parsers and writers for various file formats using a plugin interface.

Installation

Use pip, e.g.

pip install rnajena-sugar

Other installation options are described in the documentation.

Run tests with the sugar test command. Note that tests that require an Internet connection are skipped by default, this behavior can be turned off with the --web option. Also, depending on the installation and platform, some tests may be skipped or have an expected failure, to see details about the reasons please use the --verbose flag.

Getting started

Read about how to get started in the tutorial section of the documentation.

from sugar import read
seqs = read()  # load example GenBank file
print(seqs)
print(seqs[1].fts)  # show features attached to second sequence
seqs.plot_ftsviewer(show=True)  # plot attached features
aas = seqs['cds'].translate()
print(aas)
aas.write('translated_cds.fasta')

Documentation and Changelog

Documentation can be found at Read the Docs. The detailed changelog is available here.

Contributions

Contributions are welcome! -- e.g. report or fix bugs, discuss or add features, improve the documentation. See the CONTRIBUTING.md file for details.