From ca65bb13e467481f38ab7e11362c97d2b9220011 Mon Sep 17 00:00:00 2001 From: evanbiederstedt Date: Fri, 2 Aug 2019 19:12:46 -0400 Subject: [PATCH] added python shebang, and correct typo with pd.read_csv --- neoantigen.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/neoantigen.py b/neoantigen.py index d9c692e..de34222 100644 --- a/neoantigen.py +++ b/neoantigen.py @@ -1,3 +1,5 @@ +#!/usr/bin/env python + from __future__ import print_function from six.moves.configparser import ConfigParser @@ -337,7 +339,7 @@ def main(): logger.info('Starting NetMHC 4.0...') ##### # For netMHC-4 prediction, only predict on alleles for which data exists - netmhc_alleles = list(pd.read_csv(netmhc4_alleleslist, header=None, usecols=[0])[0], sep='\t') + netmhc_alleles = list(pd.read_csv(netmhc4_alleleslist, header=None, usecols=[0], sep='\t')[0]) alleles_for_prediction = list(set(netmhc_alleles) & set([x.replace(':', '') for x in hla_alleles])) logger.info('Only predicting on the following HLA-alleles: ' + ','.join(sorted(set(alleles_for_prediction))))