Added warning message when os.rmdir cannot remove temporary training directory.
Issue warning via warnings module instead of sys.stdout
Merge pull request #4 from kylebittinger/prevent-rdp-oserror

Added warning message when os.rmdir cannot remove temporary training dir
[bug fixed]: name.py might parse wrong when the species name has more than 2 words (e.g. Mustela putorius furo)
Merge pull request #10 from pm67nz/master

A fix for Issue #9 "QIIME dev does not play nice with PyCogent dev"
added a test into test_ensembl/test_host.py to check if it correctly parses a db name that contains a three words species name.
Merge pull request #12 from Skylersun/master

[FIXED]: name.py might parse wrong when the species name has more than 2 words
allow migrating alignement gaps when seqs of same length

[NEW] replaceSeqs has aa_to_codon argument, defaulting to True. This state
    allows inserting gaps from an alignment of aa's into DNA sequence alignment.
    When aa_to_codon is False, ungapped sequences must be the same length.
    Useful for getting annotations from genomes onto sliced syntenic alignments.
modify cookbook example to show aln.replaceSeqs(seqs, aa_to_codons=True) usage
gitignore tests/test_draw.py output files
Tidy up some of the drawing code a bit
Cope with zero-height sequence drawings

With a long, ungapped, featureless sequence, there is actually nothing to draw, but surrounding code still wants to know the size and scale of it.