From 1d1f5aef1d60b7bdb56b47ca734f2e78241f3262 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 23 Sep 2016 11:44:11 -0400
Subject: [PATCH] Update README
---
README.md | 19 ++++++++++++++++++-
mhcflurry/predict_command.py | 1 -
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 6ce73bd7..0af83baa 100644
--- a/README.md
+++ b/README.md
@@ -31,7 +31,24 @@ From a checkout you can run the unit tests with:
nosetests .
```
-## Making predictions
+## Making predictions from the command-line
+
+```shell
+$ mhcflurry-predict --alleles HLA-A0201 HLA-A0301 --peptides SIINFEKL SIINFEKD SIINFEKQ
+Predicting for 2 alleles and 3 peptides = 6 predictions
+allele,peptide,mhcflurry_prediction
+HLA-A0201,SIINFEKL,10672.34765625
+HLA-A0201,SIINFEKD,26042.716796875
+HLA-A0201,SIINFEKQ,26375.794921875
+HLA-A0301,SIINFEKL,25532.703125
+HLA-A0301,SIINFEKD,24997.876953125
+HLA-A0301,SIINFEKQ,28262.828125
+```
+
+You can also specify the input and output as CSV files. Run `mhcflurry-predict -h` for details.
+
+
+## Making predictions from Python
```python
from mhcflurry import predict
diff --git a/mhcflurry/predict_command.py b/mhcflurry/predict_command.py
index dec8be97..4a010402 100644
--- a/mhcflurry/predict_command.py
+++ b/mhcflurry/predict_command.py
@@ -137,7 +137,6 @@ def run(argv=sys.argv[1:]):
predictions = {} # allele -> peptide -> value
for (allele, sub_df) in df.groupby(args.allele_column):
- print(sub_df)
logging.info("Running %d predictions for allele %s" % (
len(sub_df), allele))
model = class1_allele_specific_loader.from_allele_name(allele)
--
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