sanger-sequencing 0.1.1

Getting Started

From a Python environment that has Python 3.6 or later installed you can easily

$ pip install sanger-sequencing

or use pip3 depending on your environment.

When you import the package, two main components are made available to you: a configuration class that you can instantiate to set some global configuration values and a high level analysis interface.

import sanger_sequencing

config = sanger_sequencing.Configuration()
print(config.threshold)
print(config.output)

You can read more about the meaning of those attributes in the configuration documentation. The main entry point for doing any kind of analysis is the sanger_verification function. This function requires three arguments: a template table of what to analyze, a mapping from plasmid identifiers to their sequence records (typically coming from Genbank files), and a mapping from sample identifiers to sequence records (.ab1 files).

You can find the complete documentation at: https://sanger-sequencing.readthedocs.io.

Copyright

• Copyright (c) 2018 Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark licensed under the Apache License, Version 2.0

Credits

This package was created using cookiecutter and the DD-DeCaF/cookiecutter-decaf-python project template.