Merge branch 'master' of github.com:hammerlab/mhcflurry

.gitignore

@@ -55,3 +55,6 @@ docs/_build/
 
 # PyBuilder
 target/
+
+# Data files
+*.zip

README.md

 # mhcflurry
 Peptide-MHC binding affinity prediction
 
-## Getting Started: Download, Normalize, and Combine Training Data
+## Quickstart
+
+Set up the Python environment:
+
+```
+# (set up environment)
+pip install scipy Cython
+pip install h5py
+python setup.py develop
+```
+
+Download, Normalize, and Combine Training Data:
+
+(make sure you have `wget` available, e.g. `brew install wget` on Mac OS X)
 
 ```
 scripts/download-iedb.sh
@@ -10,9 +23,23 @@ scripts/create-iedb-class1-dataset.py
 scripts/create-combined-class1-dataset.py
 ```
 
-## Getting Started: Train Neural Network Models
+## Train Neural Network Models
 
 ```
 scripts/train-class1-allele-specific-models.py
 ```
 
+This will train separate models for each HLA type.
+
+## Making predictions
+
+```python
+from mhcflurry import Mhc1BindingPredictor
+predictor = Mhc1BindingPredictor('A0201')
+predictor.predict_peptides(['SIINFEKL'])
+```
+
+```
+  Allele   Peptide  Prediction
+0  A0201  SIINFEKL  586.730529
+```