Skip to main content

Semi-automated Sanger sequence analysis for transformation verification.

Project description

https://img.shields.io/pypi/v/sanger-sequencing.svg https://img.shields.io/travis/biosustain/sanger-sequencing.svg Documentation Status Updates

Semi-automated Sanger sequence analysis for plasmid verification.

This package is the result of an internal hackathon at the Novo Nordisk Foundation Center for Biosustainability and represents our approach to improving the workflow of geneticists who need to verify plasmid constructs by Sanger sequencing.

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.

Credits

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sanger-sequencing, version 0.1.1
Filename, size File type Python version Upload date Hashes
Filename, size sanger_sequencing-0.1.1-py2.py3-none-any.whl (26.7 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size sanger-sequencing-0.1.1.tar.gz (34.3 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page