Add precalculated files to repository

Store precalculated files for 16S copy number and KO predictions in
new "data/" directory. Also, make predict_metagenomes.py and
normalize_by_copy_number.py use these files by default, so '-c' flag
is optional and not required by the user anymore.


Former-commit-id: 87ca37758a7c7116dc837bc0f067626ffd2dd6da
Update documentation for use with precalculated files

Update documentation to reflect the use of the built-in precalculated files.
No longer need to specify '-c' flag with file.
Also, move quickstart to the tutorials list.


Former-commit-id: 50c69be7fe993a7c9413ce375a4a5d1e243d5d86
Fix Greengenes name.


Former-commit-id: 19bed0ce774a195743ac9e907ddeb2008b369548
Merge pull request #15 from mlangill/add_precalculated

Add precalculated files to repository

Former-commit-id: dfacc1b73ec283040250683f461840ec6c5d519a
Merge pull request #18 from mlangill/fix_tests

Fixes many of the minor issues with test scripts

Former-commit-id: 80013fae1b34e44f614ef9dc0c50c21da0cea36d
Merge pull request #17 from mlangill/issue16

Update version to 0.0.0-dev

Former-commit-id: 9241d5b5a9fb48336de599a5366879bffc5d9669
added all_tests.py to faciliate running all tests with one command

this was modified from the version in biom-format.


Former-commit-id: 91fe63fed1a707dd18086a3fb57775fbc57e2091
Merge pull request #22 from picrust/add-all-tests

added all_tests.py to faciliate running all tests with one command

Former-commit-id: 84780770160bc4491a5f5be14d2ef41f5d3c0134
adding setup.py script

addresses issue #20.


Former-commit-id: 9ce983f6d9759682dd17ec993c02fba18e6c0f8b
Merge pull request #23 from gregcaporaso/add-setup

adding setup.py script

Former-commit-id: a670be6ad8c824639c68b01fa2e3e6138dcfb591
Remove test for unused function parse_marker_gene_copy_numbers

Addresses #8


Former-commit-id: 96995042245a342ab7dc2406ff30679318976538
Remove test_make_test_trees.py

Addresses #6 and #13
Testing is now done in test_make_test_datasets.py


Former-commit-id: f536f2eae5ff37c5b040b14891c245c50eb8e731
Remove scripts/format.py

Addresses #21


Former-commit-id: 6c9eaf5a253e12b7dfca23922ee41f69b2840dfd
Change scripts and tests to be executable

A few scripts and tests were did not have executable permissions.


Former-commit-id: 9295d581b0f68744405c7dbb5932844e6d15ef37
Remove unneeded print statements (to stdout)

Remove stdout from test_evaluate_test_datasets.py and evaluate_test_datasets.py


Former-commit-id: a8956ae96ea2f16bcd2ae2f9e996fb38620f1280
Updated labs involved to include the Vega Thurber lab


Former-commit-id: 963b1796f9198dc6d55febea328cbf704f88e3f6
Remove stdout messages from make_test_datasets.py and its test script.


Former-commit-id: 1b5e7407d0592071f9260205ad77d8fbecd7305e
Merge pull request #27 from zaneveld/readme_fix

Fixes Issue #26: Updated labs involved to include the Vega Thurber lab

Former-commit-id: e53b3f8892921d44e483867d40d6810d72c0852e
Partial Fix for Issue #29.   Biologically & formally equivalent tree representations were being rejected by the test code.  After the fix trees with swapped sister nodes are treated as OK, since the choice is arbitrary anyway.


Former-commit-id: 91c053e7f461f1daf7151b06b37b648b248aaa8f
Fixes Issue #29:  tip is replaced with tip.Name in a list comprehension prior to passing to getSubTree, which resolves test failures


Former-commit-id: dbd3ee545c0e7c468593ea010b8f42566b2ee78c