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
Fix #1092 and Fix #979
Merge branch 'master' of https://github.com/qiime/qiime into issue-1092
Removing Unifrac file conversion code as it has been ported to the FastUnfrac repo
Merge branch 'master' of git://github.com/qiime/qiime into MIENS
Ooops, forgot to delete the qiime_test_data folder for the convert_unifrac_sample_mapping_to_otu_table script
Rename script interface arguments

The naming is more standard now
Fix different aspects of the documentation

Mainly:
    - Made all lines fewer than 80 columns.
    - Change strings in the documentation to reflect the actual
      filenames that these are processing (it seems that it was still
      pointing to .txt contingency tables)

Fixes #304
Add note about the interface change.
Modifications and test additions to resolve issue #1160
Modified test and function.

There is an untested function in this code that makes boxplots. The build failed because that function called the modified function from the previous commit.
Merge branch 'master' into issue_1160
Merge branch 'master' into issue_1160
addresses #1247