pyseqan is a python interface to the SeqAn (http://www.seqan.de/) C++ sequence analysis library. pyseqan exposes functionality such as enhanced suffix arrays via an easy-to-use python interface.
pyseqan is efficient because it uses SeqAn's C++ data structures and implementation. However, its python interface is much easier to use for non-experts than SeqAn's C++ interface.
pyseqan currently exposes:
- :ref:
Simple types <simple-types>representing biological alphabets such as DNA and RNA - :ref:
Sequences <strings>over these alphabets - :ref:
Methods <seq-io>to load sequences from disk - :ref:
Indexes <indexes>such as enhanced suffix arrays for efficient look-up and search operations - :ref:
Iterators <iterators>over indexes and sequences - :ref:
Algorithms <traversal>to traverse over indexes - :ref:
Methods <disk-io>to save and load indexes to and from disk - :ref:
Methods <graphical>to visualise indexes graphically
There is much more functionality available through the SeqAn C++ API. pyseqan is extensible and this functionality will be added as the need arises. Please make requests for additions and any other comments on the Github issues page (https://github.com/JohnReid/pyseqan/issues).