MODIFIED, map_reads_to_reference supports choice of genetic_code

Modified the script with a --genetic_code option and modified the library
code to be aware of the option. Also changed the test code to include
the new option.
Merge branch 'map_reads_to_reference' of github.com:adamrp/qiime into map_reads_to_reference
modified NCBI web reference

URL is now more descriptive
Move conversion code to stand-alone lib
Fix import statement
Fix code guidelines
Correct Sample ids to be MIENS compliant
Adding more information to open reference log
Add sanity checks to parse_coords ( fixes #982 )

Add a couple checks to the coordinates parser, doing this prevents the
parser to load distance matrices seamlessly. Specifically the function
will now check for:
    - First line being the number of vectors.
    - Second to last line being eigenvalues.
    - Last line being the percentage of variation explained.

When these conditions are not mete a `QiimeParseError` exception is
raised; the test suite was extended to check it raises these errors on
different cases.
Remove extra percent sign in coordinates string

This percent sign would have only be needed if the string was being
formatted.
Fix #1092 and Fix #979
fix #1110 changed to say files are whitespace separated not tab separated
fix #1150 updated -h documentation
changes recommeded by @gregcaporasso
Ignore extra samples when performing sanity checks

Fixes #1120.
Fix filename extensions in alpha_diversity.py

When invoked in batch-processing mode, the output filenames will now have a .txt extension instead of .biom. Fixes #1147.
Erroneous error message in split_libraries_fastq

The option mentioned in the error message should be
  --barcode_read_fps
instead of
  --barcode_fps
Slight modification to text in log file, added percent of total seqs demultiplexed, added unit test for demultiplex_fasta.py
Added 2 histogram formatting code to qiime/format.py and unit test, in preparation for use with new quality_filter_fasta.py code
uclust picker handles filenames with multiple dots

Intermediate .uc files are now correctly named based on the input sequences filename, including the case where there are multiple dots in the filename.

Also updated QIIME codebase to use uclust.py in pycogent_backports/ (was previously only being used in assign_taxonomy.py).

Fixes #191.