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.
addresses #1247
Merge branch 'master' of git://github.com/qiime/qiime into MIENS

Conflicts:
	qiime/parse.py
	tests/test_parse.py
parse_coords is now more flexible on input type
Update downstream.py to ammend interface changes

The command call to summarize_otu_by_category.py would fail because some
option names were changed.
Merge branch 'master' of git://github.com/qiime/qiime into issue_304

Conflicts:
	ChangeLog.md
wasn't checking for an empty line correctly
Merge branch 'master' of git://github.com/qiime/qiime into MIENS
Changes added to ChangeLog