remove example, clean README

README.md

@@ -7,7 +7,10 @@
 
 Quantitative analysis of the function and taxonomy of microbiomes and their interaction.
 
-# Setup
+
+# Developers
+
+## Setup
 
 The newest version of metaquantome should be downloaded from this site.
 The dependencies are most easily satisfied with conda, and the environment can
@@ -21,53 +24,9 @@ source activate metaquantome
 Note that the bioconda and conda forge channels must be enabled,
 as described on [the bioconda website](https://bioconda.github.io/#set-up-channels).
 
-# Tests
+## Tests
 To run unittests for the project, run the following from the root directory:
 
 ```sh
 python -m unittest discover tests
 ```
-
-# Basic usage
-
-We can use example files within the `examples` directory to demonstrate the use of the command line.
-
-```sh
-python3 cli.py expand -m f \
-    --pep_colname peptide --outfile test.tmp -i example/int.tab \
-    --func_file example/func.tab  --func_colname go --ontology go \
-    --samps '{"s1": ["int1", "int2", "int3"], "s2": ["int4", "int5", "int6"]}'
-```
-
-# Roadmap
-
-## High Priority
-- visualizations
-- documentation
-- better arg checking
-    - deal with sample that is completely missing values
-    - deal with missing values better
-    - taxonomy rank checking
-    - move ncbi checking to IO
-    - check that supplied columns are in the dataframe
-    - check that sample info provides a list, or is coerced to a list
-    - don't return above phylum
-    - don't return BP, MF, or CC
-    - raise error when all rows are filtered out
-    - strip any newlines in samps file
-- configure Travis CI on Github
-
-
-## Lower Priority
-- benchmarking and optimization
-- use flake8 for codestyle
-
-## Done
-- unified database structure and 'adding up'
-    - unify this with classes
-    - work on EC in particular
-    - how do we implement for COG cats?
-- add handling if description is not found in database (EC)
-- switch to metagenomics slim
-- add option for specific rank in TF
-- move threshold to calculating mean values as well