biocore/scikit-bio — pull request #705 by jairideout (2014-10-15 18:18:24+00:00)
Title: add FASTA format support to I/O registry

**Not ready for merge:** This pull request overhauls how FASTA I/O is performed in scikit-bio, and the underlying readers/writers have been rewritten in the process to better support the usage of scikit-bio's sequence data classes. I'd like to compare performance of current vs new implementations before merge.

Added the following FASTA file support:
- Detailed docs describing the format
- Automatic file format detection via a FASTA sniffer
- FASTA files can be read into and written from ``SequenceCollection``, ``Alignment``, ``BiologicalSequence``, ``NucleotideSequence``, ``DNASequence``, ``RNASequence``, and ``ProteinSequence`` objects via ``read`` and ``write`` methods
- FASTA files can be streamed into and out of memory via ``skbio.io.read`` and ``skbio.io.write``. These generators yield ``BiologicalSequence`` objects (or subclasses)

Deprecated the current readers/writers for removal in scikit-bio 0.3.0. Please see the changelog for more details.

Fixes #678. @ebolyen can you take the first pass through this?