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Multi-profile files using HDF5

Martijn Vermaat requested to merge wip/hdf5 into master

The following is still todo, but will be done after this merge request.

  • Describe the file format version 1.0.0 (single k per file, all strings unicode, etc). This will go with #3 (closed).
  • Get rid of the from math import * in k_mer.kmer. This will go together with a small reworking of the custom function arguments. The approach in Wiggelen is more general.
  • Modifying existing profile files.
  • Option to index by record on one fasta file.
  • Read files other than FASTA files (should be easy with BioPython).
  • Read compressed FASTA files.
  • Don't load entire profile for info command.

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