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.
The goal is to be fast so most everthing is written in Cython or C.
fileio
: genbank and fasta reader/writers, xmfaseqrecord
: less featured replacement for Biopython SeqRecordseqstr
: Reverse Complement and Hamming Distance findersseqgraph
: find cliques of compatible sequencesseqint
: convert sequences less than 32 bases to binaryseqscreen
: filter sequences based on things like GC contentseqsearch
: search sequences for features like restriction sites or "submers" (kmers with 0 or more mismatches to a subsequence in the target)
- Run
python setup.py build_ext --inplace
to build in the package dir - Optional flag "--rmbuilt" removes old *.c and *.so files from previous builds