libnano 0.2.3.0

Low-level nucleic acid sequence manipulation tools

libnano is beta

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