Reproducible output.

.gitignore

 *.pyc
 *.egg-info
-build
-dist
-.ipynb_checkpoints
+build/
+dist/
+.ipynb_checkpoints/
+.cache/
+.tox/

backtranslate/cli.py

@@ -30,7 +30,7 @@ def with_dna(input_handle, output_handle, offset, position, amino_acid):
     codon = reference[codon_pos:codon_pos + 3]
     substitutions = bt.with_dna(codon, protein_letters_3to1[amino_acid])
 
-    for subst in subst_to_cds(substitutions, (position - 1) * 3):
+    for subst in sorted(subst_to_cds(substitutions, (position - 1) * 3)):
         output_handle.write('{}\t{}\t{}\n'.format(*subst))
 
 
@@ -58,7 +58,7 @@ def without_dna(output_handle, position, reference_amino_acid, amino_acid):
         output_handle.write(
             'This substitution can be improved by using `with_dna`.\n')
 
-    for subst in subst_to_cds(substitutions, (position - 1) * 3):
+    for subst in sorted(subst_to_cds(substitutions, (position - 1) * 3)):
         output_handle.write('{}\t{}\t{}\n'.format(*subst))
 
 
@@ -79,14 +79,15 @@ def find_stops(input_handle, output_handle, offset, compact):
 
         for position in stop_positions:
             if not compact:
-                for subst in stop_positions[position]:
+                for subst in sorted(stop_positions[position]):
                     output_handle.write('{}\t{}\t{}\n'.format(
                         offset + (index * 3) + position, *subst))
             else:
                 output_handle.write('{}\t{}\t{}\n'.format(
                     offset + (index * 3) + position,
                     list(stop_positions[position])[0][0],
-                    ','.join(map(lambda x: x[1], stop_positions[position]))))
+                    ','.join(map(lambda x: x[1],
+                    sorted(stop_positions[position])))))
 
 
 def main():

backtranslate/util.py

@@ -11,8 +11,8 @@ def _three_to_one():
 
     :returns dict: Three letter to one letter amino acids table.
     """
-    return dict(map(lambda x: (str(x[0]), str(x[1])),
-        IUPACData.protein_letters_3to1_extended.items()) + [('Ter', '*')])
+    return dict(list(map(lambda x: (str(x[0]), str(x[1])),
+        IUPACData.protein_letters_3to1_extended.items()) + [('Ter', '*')]))
 
 
 def subst_to_cds(substitutions, offset):

setup.py

@@ -12,6 +12,7 @@ license = 'MIT License'
 keywords = ['bioinformatics']
 
 dependencies = ['biopython', 'future', 'python-Levenshtein']
+develop_dependencies = ['pytest', 'tox']
 supported = [(2, 7), (3, 3), (3, 4)]
 classifiers = [
     'Development Status :: 3 - Alpha',
@@ -71,6 +72,7 @@ setup(
     platforms=['any'],
     packages=[package],
     install_requires=dependencies,
+    tests_require=develop_dependencies,
     entry_points={
         'console_scripts': ['{0} = {0}.cli:main'.format(package)]
     },

tests/test_cli.py

@@ -5,14 +5,16 @@ from __future__ import (
     absolute_import, division, print_function, unicode_literals)
 from future.builtins import str, zip
 
-import StringIO
-import md5
+import sys
+
+from hashlib import md5
+from io import StringIO
 
 from backtranslate import cli
 
 
 def md5_check(data, md5sum):
-    return md5.md5(data).hexdigest() == md5sum
+    return md5(data).hexdigest() == md5sum
 
 
 class TestParser(object):
@@ -21,7 +23,7 @@ class TestParser(object):
     """
     def setup(self):
         self._input = open('data/mhv.fa')
-        self._output = StringIO.StringIO()
+        self._output = StringIO()
 
     def test_with_dna(self):
         cli.with_dna(self._input, self._output, 210, 1, 'Leu')
@@ -36,9 +38,9 @@ class TestParser(object):
     def test_find_stops(self):
         cli.find_stops(self._input, self._output, 210, False)
         assert md5_check(
-            self._output.getvalue(), 'b3dbcc94594ab61e36dbb2256d4b4561')
+            self._output.getvalue(), '41c105e384651201970c0b2efd3afa3e')
 
     def test_find_stops_compact(self):
         cli.find_stops(self._input, self._output, 210, True)
         assert md5_check(
-            self._output.getvalue(), '34aa553f2ea72ca992b2568a963c27ee')
+            self._output.getvalue(), '67c62854f4c0972e3fbf3dcec81b6a94')

tox.ini

+[tox]
+envlist = py27,py34
+
+[testenv]
+commands = py.test
+whitelist_externals = py.test