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, xmfa
• seqrecord: less featured replacement for Biopython SeqRecord
• 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
• seqsearch: 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