Prank: PEP8 whitespace cleanup.

Bio/Align/Applications/_Prank.py

@@ -46,7 +46,7 @@ class PrankCommandline(AbstractCommandline):
     Last checked against version: 081202
     """
     def __init__(self, cmd="prank", **kwargs):
-        OUTPUT_FORMAT_VALUES = list(range(1,18))
+        OUTPUT_FORMAT_VALUES = list(range(1, 18))
         self.parameters = [
             ################## input/output parameters: ##################
             #-d=sequence_file
@@ -55,7 +55,7 @@ def __init__(self, cmd="prank", **kwargs):
                     filename=True,
                     is_required=True),
             #-t=tree_file [default: no tree, generate approximate NJ tree]
-            _Option(["-t", "t"],"Input guide tree filename",
+            _Option(["-t", "t"], "Input guide tree filename",
                     filename=True),
             #-tree="tree_string" [tree in newick format; in double quotes]
             _Option(["-tree", "tree"],
@@ -193,7 +193,7 @@ def __init__(self, cmd="prank", **kwargs):
             _Switch(["-convert", "convert"],
                     "Convert input alignment to new format. Do "
                     "not perform alignment")
-            ]
+        ]
         AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

Tests/test_Prank_tool.py

@@ -19,7 +19,7 @@
 os.environ['LANG'] = 'C'
 
 prank_exe = None
-if sys.platform=="win32":
+if sys.platform == "win32":
     try:
         #This can vary depending on the Windows language.
         prog_files = os.environ["PROGRAMFILES"]
@@ -30,7 +30,7 @@
     #sensible locations under Program Files... and then the full path.
     likely_dirs = ["",  # Current dir
                    prog_files,
-                   os.path.join(prog_files,"Prank")] + sys.path
+                   os.path.join(prog_files, "Prank")] + sys.path
     for folder in likely_dirs:
         if os.path.isdir(folder):
             if os.path.isfile(os.path.join(folder, "prank.exe")):
@@ -90,12 +90,12 @@ def test_Prank_simple_with_NEXUS_output(self):
         """Simple round-trip through app with infile, output in NEXUS
         output.?.??? files written to cwd - no way to redirect
         """
-        records = list(SeqIO.parse(self.infile1,"fasta"))
+        records = list(SeqIO.parse(self.infile1, "fasta"))
         #Try using keyword argument,
         cmdline = PrankCommandline(prank_exe, d=self.infile1, noxml=True)
         #Try using a property,
         cmdline.d = self.infile1
-        cmdline.f = 17 # NEXUS format
+        cmdline.f = 17  # NEXUS format
         cmdline.set_parameter("notree", True)
         self.assertEqual(str(cmdline), prank_exe +
                          " -d=Fasta/fa01 -f=17 -noxml -notree")
@@ -107,10 +107,10 @@ def test_Prank_simple_with_NEXUS_output(self):
             align = AlignIO.read("output.2.nex", "nexus")
             for old, new in zip(records, align):
                 #Old versions of Prank reduced name to 9 chars
-                self.assertTrue(old.id==new.id or old.id[:9]==new.id)
+                self.assertTrue(old.id == new.id or old.id[:9] == new.id)
                 #infile1 has alignment gaps in it
-                self.assertEqual(str(new.seq).replace("-",""),
-                                 str(old.seq).replace("-",""))
+                self.assertEqual(str(new.seq).replace("-", ""),
+                                 str(old.seq).replace("-", ""))
         except NexusError:
             #See bug 3119,
             #Bio.Nexus can't parse output from prank v100701 (1 July 2010)
@@ -165,7 +165,7 @@ def conversion(self, prank_number, prank_ext, format):
         self.assertTrue(os.path.isfile(filename))
         old = AlignIO.read(self.input, "fasta")
         #Hack...
-        if format=="phylip":
+        if format == "phylip":
             for record in old:
                 record.id = record.id[:10]
         new = AlignIO.read(filename, format)
@@ -197,5 +197,5 @@ def test_convert_to_phylip(self):
 
 
 if __name__ == "__main__":
-    runner = unittest.TextTestRunner(verbosity = 2)
+    runner = unittest.TextTestRunner(verbosity=2)
     unittest.main(testRunner=runner)