Skip to main content

Low-level nucleic acid sequence manipulation tools

Project description

libnano is beta

https://secure.travis-ci.org/libnano/libnano.png https://img.shields.io/pypi/l/libnano.png https://img.shields.io/pypi/v/libnano.png

nucleic acid toolkit

Low level Python modules for working with DNA sequences
It was developed to be used as a cog in application specific libraries while avoiding bloat.<br/>
The goal is to be fast so most many things are written in Cython or C.
This project is under active development, and hopefully documentation will by done soon
Python 3.6+ only now as the code base is typed for Cython and type-hinted for Python code

Features

  • seqstr: Reverse Complement and Hamming Distance finders
  • seqgraph: find cliques of compatible sequences
  • seqint: convert sequences less than 32 bases to binary
  • seqscreen: filter sequences based on things like GC content
  • ensemblrest: Use the Ensembl REST API to look up gene and transcript information
  • prostr: work with converting DNA to RNA to AA and back again
  • barcode_tools: generate DNA barcode sets with length and Hamming distance restrictions
  • seqsearch: search sequences for features like restriction sites or “submers” (kmers with 0 or more mismatches to a subsequence in the target)
  • fileio: genbank and fasta reader/writers, xmfa
  • seqrecord: less featured replacement for Biopython SeqRecord

Installation

If you would like to install libnano in your local Python environment you may use pip:

$ pip install libnano

or build from source from Github repo

$ python setup.py install

Project details


Download files

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

Filename, size & hash SHA256 hash help File type Python version Upload date
libnano-0.2.3.0-cp36-cp36m-macosx_10_10_x86_64.whl (874.6 kB) Copy SHA256 hash SHA256 Wheel cp36
libnano-0.2.3.0-cp36-cp36m-win_amd64.whl (873.8 kB) Copy SHA256 hash SHA256 Wheel cp36
libnano-0.2.3.0.tar.gz (1.7 MB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page