The pyseqan python package

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.

Efficiency and ease-of-use

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.

Functionality

pyseqan currently exposes:

  • Simple types representing biological alphabets such as DNA and RNA
  • Sequences over these alphabets
  • Methods to load sequences from disk
  • Indexes such as enhanced suffix arrays for efficient look-up and search operations
  • Iterators over indexes and sequences
  • Algorithms to traverse over indexes
  • Methods to save and load indexes to and from disk
  • Methods 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).

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