Warning: You are using the test version of PyPI. This is a pre-production deployment of Warehouse. Changes made here affect the production instance of TestPyPI (testpypi.python.org).
Help us improve Python packaging - Donate today!

A tool kit for accessing NCBI's GenBank

Project Description

NCBI Tool Kit

A tool kit for downloading and curating collections of genomes retrieved from the National Center for Biotechology Information’s public database, GenBank.

Requires rsync. Tested only with rsync version 3.1.2 protocol version 31.

Installation

Using pip:

pip install ncbitk

Or:

git clone https://github.com/andrewsanchez/NCBITK.git
python setup.py install

Regardless of which installation method you choose, I recommend using a virtual environment.

Basic Usage

Download all GenBank bacteria:

ncbitk [directory] --update

If you have already run NCBITK, the above will also update your local collection, i.e. remove old genomes no longer in the assembly summary and download the latest assembly versions.

Get the status of your collection:

ncbitk [directory] --status

This will tell you how many genomes you have, what is missing from your collection, and how many deprecated genomes are present.

Release History

Release History

This version
History Node

1.0a15

History Node

1.0a14

History Node

1.0a13

History Node

1.0a12

History Node

1.0a11

History Node

1.0a4

Download Files

Download Files

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

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
NCBITK-1.0a15.tar.gz (6.5 kB) Copy SHA256 Checksum SHA256 Source May 19, 2017

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting