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
- 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
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