From 9ef82bae0b9da8b509e150f18ff3fa3c52247b56 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Mon, 9 Jan 2017 14:25:46 -0500
Subject: [PATCH] allow commas in peptide and allele strings for
mhcflurry-predict, incrememented keras version
---
mhcflurry/predict_command.py | 15 +++++++++++++--
requirements.txt | 2 +-
setup.py | 2 +-
3 files changed, 15 insertions(+), 4 deletions(-)
diff --git a/mhcflurry/predict_command.py b/mhcflurry/predict_command.py
index 4a010402..edcc6af0 100644
--- a/mhcflurry/predict_command.py
+++ b/mhcflurry/predict_command.py
@@ -122,8 +122,19 @@ def run(argv=sys.argv[1:]):
parser.error(
"Specify either an input CSV file or both the "
"--alleles and --peptides arguments")
-
- pairs = list(itertools.product(args.alleles, args.peptides))
+ # split user specified allele and peptide strings in case they
+ # contain multiple entries separated by commas
+ alleles = []
+ for allele_string in args.alleles:
+ alleles.extend([s.strip() for s in allele_string.split(",")])
+ peptides = []
+ for peptide in args.peptides:
+ peptides.extend(peptide.strip() for p in peptide.split(","))
+ for peptide in peptides:
+ if not peptide.isalpha():
+ raise ValueError(
+ "Unexpected character(s) in peptide '%s'" % peptide)
+ pairs = list(itertools.product(alleles, peptides))
df = pandas.DataFrame({
"allele": [p[0] for p in pairs],
"peptide": [p[1] for p in pairs],
diff --git a/requirements.txt b/requirements.txt
index 78a52a93..e1768825 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,7 @@ numpy>= 1.11
pandas>=0.13.1
appdirs
theano>=0.8.2
-keras==1.1.0
+keras==1.2.0
fancyimpute>=0.0.12
scikit-learn
h5py
diff --git a/setup.py b/setup.py
index 1571028c..422d2eca 100644
--- a/setup.py
+++ b/setup.py
@@ -53,7 +53,7 @@ if __name__ == '__main__':
'pandas>=0.13.1',
'appdirs',
'theano>=0.8.2',
- 'keras==1.1.0',
+ 'keras==1.2.0',
'fancyimpute>=0.0.12',
'scikit-learn',
'h5py',
--
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