Adding unit test for new NCBI BLAST wrappers

Tests/test_NCBI_BLAST_tools.py

@@ -0,0 +1,129 @@
+# Copyright 2009 by Peter Cock.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+#
+# This unit test attempts to locate the blastall executable and the nr
+# database, and if it finds them then do some standalone blast searches
+# using Bio.Blast.NCBIStandalone to call the command line tool.
+
+import os, sys
+import subprocess
+import unittest
+
+from Bio import MissingExternalDependencyError
+from Bio.Blast import Applications
+
+# TODO - On windows, can we use the ncbi.ini file?
+wanted = ["blastx", "blastp", "blastn", "tblastn", "tblastx",
+          "rpsblast", "rpstblastn", "psiblast"]
+exe_names = {}
+
+if sys.platform=="win32":
+    try:
+        #This can vary depending on the Windows language.
+        prog_files = os.environ["PROGRAMFILES"]
+    except KeyError:
+        prog_files = r"C:\Program Files"
+    likely_dirs = ["", #Current dir
+                   prog_files,
+                   #TODO - Check what the installer does...
+                   os.path.join(prog_files,"NCBI-BLAST"),
+                   os.path.join(prog_files,"NCBI-BLAST+"),
+                   os.path.join(prog_files,"BLAST+"),
+                   os.path.join(prog_files,"BLAST")] + sys.path
+    for folder in likely_dirs:
+        if os.path.isdir(folder):
+            for name in wanted :
+                if os.path.isfile(os.path.join(folder, name+".exe")):
+                    exe_names[name] = os.path.join(folder, name+".exe")
+        if muscle_exe : break
+else:
+    import commands
+    for name in wanted :
+        output = commands.getoutput("%s -h" % name)
+        #NOTE - check for "ERROR: Invalid argument: -h" to tell the old
+        #and new rpsblast apart
+        if "not found" not in output and "BLAST" in output.upper() \
+        and "ERROR: Invalid argument: -h" not in output:
+            exe_names[name] = name
+if len(exe_names) < len(wanted) :
+    raise MissingExternalDependencyError("Install the NCBI BLAST+ command line tools "
+                                         "if you want to use the "
+                                         "Bio.Blast.Applications wrapper.")
+
+class CheckCompleteArgList(unittest.TestCase):
+    def check(self, exe_name, wrapper) :
+        global exe_names
+        exe = exe_names[exe_name]
+        cline = wrapper(exe, h=True)
+
+        names = set(parameter.names[0] \
+                    for parameter in cline.parameters)
+
+        child = subprocess.Popen(str(cline),
+                                 stdout=subprocess.PIPE,
+                                 stderr=subprocess.PIPE,
+                                 shell=(sys.platform!="win32"))
+        stdoutdata, stderrdata = child.communicate()
+        self.assertEqual(stderrdata, "",
+                         "%s\n%s" % (str(cline), stderrdata))
+        names_in_tool = set()
+        while stdoutdata :
+            index = stdoutdata.find("[")
+            if index == -1 : break
+            stdoutdata = stdoutdata[index+1:]
+            index = stdoutdata.find("]")
+            assert index != -1
+            name = stdoutdata[:index]
+            if " " in name : name = name.split(None,1)[0]
+            names_in_tool.add(name)
+            stdoutdata = stdoutdata[index+1:]
+
+        extra = names.difference(names_in_tool)
+        missing = names_in_tool.difference(names)
+        if extra or missing :
+            print "Extra: " + ",".join(sorted(extra))
+            print "Missing: " + ",".join(sorted(missing))
+
+        self.assertEqual(len(extra), 0, \
+                         "Wrapper has extra: " + ", ".join(sorted(extra)))
+        self.assertEqual(len(missing), 0, \
+                         "Wrapper is missing: " + ", ".join(sorted(missing)))
+
+    def test_blastx(self):
+        """Check all blastx arguments are supported"""
+        self.check("blastx", Applications.NcbiblastxCommandline)
+
+    def test_blastp(self):
+        """Check all blastp arguments are supported"""
+        self.check("blastp", Applications.NcbiblastpCommandline)
+
+    def test_blastn(self):
+        """Check all blastn arguments are supported"""
+        self.check("blastn", Applications.NcbiblastnCommandline)
+
+    def test_tblastx(self):
+        """Check all tblastx arguments are supported"""
+        self.check("tblastx", Applications.NcbitblastxCommandline)
+
+    def test_tblastn(self):
+        """Check all tblastn arguments are supported"""
+        self.check("tblastn", Applications.NcbitblastnCommandline)
+
+    def test_psiblast(self):
+        """Check all psiblast arguments are supported"""
+        self.check("psiblast", Applications.NcbipsiblastCommandline)
+
+    def test_rpsblast(self):
+        """Check all rpsblast arguments are supported"""
+        self.check("rpsblast", Applications.NcbirpsblastCommandline)
+
+    def test_rpstblastn(self):
+        """Check all rpstblastn arguments are supported"""
+        self.check("rpstblastn", Applications.NcbirpstblastnCommandline)
+
+
+if __name__ == "__main__":
+    runner = unittest.TextTestRunner(verbosity = 2)
+    unittest.main(testRunner=runner)