Change test to pytest package

MakeBlastDB.py

@@ -71,12 +71,12 @@ class MakeBlastDB(object):
             if proc.returncode == 1:
                 msg = "An error occured during execution of following command :\n"
                 msg += "COMMAND : {}\n".format(cmd)
-                msg += "STDERR : {}\n".format(stderr)
+                msg += "STDERR : {}\n".format(stderr.strip())
                 raise Exception (msg)
 
             # Verify the output
             if not stdout:
-                raise Exception ("Error, no data received from standard output\n"+stderr)
+                raise Exception ("Error, no data received from standard output\n{}\n".format(stderr.strip()))
 
             return path.abspath(db_path)
 
@@ -89,4 +89,4 @@ class MakeBlastDB(object):
                 if path.isfile (f):
                     remove (f)
 
-            raise Exception (E.message+"Impossible to generate a valid database from the reference sequence")
+            raise Exception (str(E)+"Impossible to generate a valid database from the reference sequence")

README.md

 # pyBlast
-Python 2.7 wrapper for ncbi blast+
+
+Python 2.7/3.3 wrapper for ncbi blast+
+
+## Test
+
+* Install pytest
+* Run test with py.test-2.7  -v
\ No newline at end of file

UniTest.py

-#!/usr/bin/env python2.7
-# -*- coding: utf-8 -*-
-
-import random
-import string
-
-if __name__ == '__main__':
-
-    msg = ""
-
-    ###############################################################################################
-
-    print ("Testing MakeBlastDB")
-    try:
-        from MakeBlastDB import MakeBlastDB
-        db_maker = MakeBlastDB()
-        db_path = db_maker (ref_path="./test/Reference.fa" , db_path="./test/Reference")
-        msg += "PASS\t MakeBlastDB test\n"
-    except Exception as E:
-        msg += "FAIL\t MakeBlastDB test\t {}\n".format(E)
-
-    ###############################################################################################
-
-    print ("Testing BlastHit")
-    try:
-        from BlastHit import BlastHit
-        hit_list = []
-        for i in range (100):
-            hit_list .append(BlastHit (
-                q_id = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(10)),
-                s_id = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(10)),
-                identity = random.uniform(0, 1),
-                length = random.randint(1, 100),
-                mis = random.randint(0, 100),
-                gap = random.randint(0, 100),
-                q_start = random.randint(0, 100),
-                q_end = random.randint(0, 100),
-                s_start = random.randint(0, 100),
-                s_end = random.randint(0, 100),
-                evalue = random.uniform(0, 1),
-                bscore = random.uniform(0, 1),
-                qseq = ''.join(random.choice(["A","T","C","G"]) for _ in range(20))))
-        assert len(hit_list) == 100, "Incorect number of hit generated"
-        msg += "PASS\t BlastHit test\n"
-    except Exception as E:
-        msg += "FAIL\t BlastHit test\t {}\n".format(E)
-
-    ###############################################################################################
-
-    print ("Testing MakeBlastn")
-    try:
-        from MakeBlastn import MakeBlastn
-        for _ in range (50):
-            blast_maker = MakeBlastn (
-                task = random.choice(['blastn', 'blastn-short', 'dc-megablast', 'megablast', 'rmblastn']),
-                evalue = random.uniform(0, 1),
-                best_per_query_seq = random.choice([True, False]))
-            hits = blast_maker(query_path = "./test/query_sample.fa", db_path = db_path)
-
-        msg += "PASS\t MakeBlastn test\n"
-    except Exception as E:
-        msg += "FAIL\t MakeBlastn test\t {}\n".format(E)
-
-    print (msg)
-
-    ###############################################################################################

test_pyBlast.py

+# -*- coding: utf-8 -*-
+
+"""
+@package    pyBlast
+@brief      Test function to be used with python package pytest
+@copyright  [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
+@author     Adrien Leger - 2014
+* <adrien.leger@gmail.com> <adrien.leger@inserm.fr> <adrien.leger@univ-nantes.fr>
+* [Github](https://github.com/a-slide)
+* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
+"""
+
+# Standard library packages import
+import sys, os, random, string
+
+# Third party packages import
+import pytest
+
+# Import the current working dir in the python path to allow local package imports
+sys.path.append(os.getcwd())
+
+# Start tests
+def test_MakeBlastDB():
+    from MakeBlastDB import MakeBlastDB
+    db_maker = MakeBlastDB()
+    assert(db_maker (
+            ref_path="./test/Reference.fa" ,
+            db_path="./test/Reference"))
+
+def test_BlastHit():
+    from BlastHit import BlastHit
+    for _ in range (100):
+        assert(BlastHit(
+                q_id = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(10)),
+                s_id = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(10)),
+                identity = random.uniform(0, 1),
+                length = random.randint(1, 100),
+                mis = random.randint(0, 100),
+                gap = random.randint(0, 100),
+                q_start = random.randint(0, 100),
+                q_end = random.randint(0, 100),
+                s_start = random.randint(0, 100),
+                s_end = random.randint(0, 100),
+                evalue = random.uniform(0, 1),
+                bscore = random.uniform(0, 100),
+                qseq = ''.join(random.choice(["A","T","C","G"]) for _ in range(20))))
+
+def test_MakeBlastn():
+    from MakeBlastn import MakeBlastn
+    for _ in range (10):
+        blast_maker = MakeBlastn(
+            task = random.choice(['blastn', 'blastn-short', 'dc-megablast', 'megablast', 'rmblastn']),
+            evalue = random.uniform(0, 1),
+            best_per_query_seq = random.choice([True, False]))
+
+        assert(blast_maker(
+                query_path="./test/query_sample.fa",
+                db_path="./test/Reference" ))