minor

Author: dmnfarrell

basics.ipynb

@@ -21,7 +21,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 9,
    "metadata": {
     "collapsed": false
    },
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 10,
    "metadata": {
     "collapsed": true
    },

setup.py

@@ -1,7 +1,5 @@
-
 from setuptools import setup
 import sys,os
-home=os.path.expanduser('~')
 
 setup(
     name = 'epitopepredict',
@@ -12,7 +10,8 @@
     author = 'Damien Farrell',
     author_email = 'farrell.damien[at]gmail.com',
     packages = ['epitopepredict'],
-    package_data={'epitopepredict': ['mhcdata/*.csv','tepitope/*.txt','tepitope/pssm/*']},
+    package_data={'epitopepredict': ['mhcdata/*.csv','tepitope/*.txt',
+				     'tepitope/pssm/*']},
     install_requires=['numpy>=1.5',
                       'pandas>=0.17',
                       'biopython>=1.5'],
@@ -22,7 +21,7 @@
             'Operating System :: MacOS :: MacOS X',
             'Operating System :: Microsoft :: Windows',
             'Operating System :: POSIX',
-            'License :: OSI Approved :: Apache License v2',
+            'License :: OSI Approved :: Apache Software License',
             'Development Status :: 4 - Beta',
             'Intended Audience :: Science/Research'],
     keywords = ['epitope','mhc','immunology','biology'],

testing/mhc1_common.csv

@@ -0,0 +1,31 @@
+allele,percent
+HLA-A*02:01,0.46
+HLA-C*07:01,0.28
+HLA-A*01:01,0.27
+HLA-A*03:01,0.24
+HLA-C*07:02,0.22
+HLA-C*04:01,0.21
+HLA-B*44:02,0.20
+HLA-B*07:02,0.18
+HLA-B*08:01,0.18
+HLA-C*05:01,0.17
+HLA-C*03:04,16.8
+HLA-C*06:02,15.7
+HLA-A*11:01,15.3
+HLA-B*40:01,13.6
+HLA-A*24:02,12.1
+HLA-B*35:01,10.7
+HLA-C*03:03,10.6
+HLA-B*51:01,10.4
+HLA-C*12:03,9.9
+HLA-B*15:01,9.6
+HLA-A*29:02,8.9
+HLA-A*26:01,8.2
+HLA-A*32:01,8.2
+HLA-C*08:02,7.7
+HLA-A*25:01,7.5
+HLA-B*57:01,7.1
+HLA-B*14:02,6.7
+HLA-C*02:02,6.6
+HLA-B*18:01,6.4
+HLA-B*44:03,6.4