Updated Record class in Bio.SCOP.Cla to use a dictionary instead of a…

… list of pairs, because the file format definition specified by the maintainers of SCOP states that the order of the key-value pairs in the hierarchy field of the Record does not matter.

Also updated the string representation of the Record so that it does not end with a newline character.

Updated tests accordingly.

Bio/SCOP/Cla.py

@@ -1,4 +1,5 @@
 # Copyright 2001 by Gavin E. Crooks.  All rights reserved.
+# Copyright 2010 Jeffrey Finkelstein
 # 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.
@@ -40,7 +41,7 @@ def __init__(self, line=None):
         self.residues = None 
         self.sccs = ''
         self.sunid =''
-        self.hierarchy = []
+        self.hierarchy = {}
         if line:
             self._process(line)
 
@@ -57,8 +58,7 @@ def _process(self, line):
 
         for ht in hierarchy.split(","):
             key, value = ht.split('=')
-            value = int(value)
-            self.hierarchy.append([key, value])
+            self.hierarchy[key] = int(value)
 
     def __str__(self):
         s = []
@@ -67,12 +67,10 @@ def __str__(self):
         s.append(self.sccs)
         s.append(self.sunid)
 
-        h=[]
-        for ht in self.hierarchy:
-            h.append("=".join(map(str,ht))) 
-        s.append(",".join(h))
+        s.append(",".join([key + '=' + str(value) for key, value \
+                               in self.hierarchy.items()]))
 
-        return "\t".join(map(str,s)) + "\n"
+        return "\t".join(map(str,s)) #+ "\n"
 
 
 def parse(handle):

Bio/SCOP/__init__.py

@@ -1,5 +1,6 @@
 # Copyright 2001 by Gavin E. Crooks.  All rights reserved.
 # Modifications Copyright 2004/2005 James Casbon. All rights Reserved.
+# Copyright 2010 Jeffrey Finkelstein
 #
 # This code is part of the Biopython distribution and governed by its
 # license.  Please see the LICENSE file that should have been included
@@ -318,8 +319,7 @@ def write_cla(self, handle):
         nodes = self._sidDict.values()
         # We order nodes to ease comparison with original file
         nodes.sort(key = lambda n: n.sunid)
-        for n in nodes:
-            handle.write(str(n.toClaRecord()))
+        handle.writelines([str(n.toClaRecord()) + '\n' for n in nodes])
 
 
     def getDomainFromSQL(self, sunid=None, sid=None):
@@ -661,10 +661,12 @@ def toClaRecord(self):
 
         n = self
         while n.sunid != 0: #Not root node
-            rec.hierarchy.append( (n.type, str(n.sunid)) )
+            rec.hierarchy[n.type] = n.sunid
             n = n.getParent()
 
-        rec.hierarchy.reverse()
+        # Order does not matter in the hierarchy field. For more info, see
+        # http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html
+        #rec.hierarchy.reverse()
 
         return rec
 

CONTRIB

@@ -29,6 +29,7 @@ Andrew Dalke <dalke at domain acm.org>
 Michiel de Hoon <mdehoon at domain c2b2.columbia.edu>
 Sjoerd de Vries <sjoerd at domain nmr.chem.uu.nl>
 Kyle Ellrott
+Jeffrey Finkelstein <jeffrey.finkelstein@gmail.com>
 Iddo Friedberg <idoerg at domain burnham.org>
 Bertrand Frottier <bertrand.frottier at domain free.fr>
 Frederik Gwinner

Tests/test_SCOP_Cla.py

@@ -1,4 +1,5 @@
 # Copyright 2001 by Gavin E. Crooks.  All rights reserved.
+# Copyright 2010 Jeffrey Finkelstein
 # 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.
@@ -36,8 +37,20 @@ def testStr(self):
         try: 
             for line in f:
                 record = Cla.Record(line)
-                #End of line is platform dependent. Strip it off
-                self.assertEqual(str(record).rstrip(), line.rstrip())
+                # The SCOP Classification file format which can be found at
+                # http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html states
+                # that the list of classification hierarchy key-value pairs is
+                # unordered, therefore we need only check that they are all
+                # there, NOT that they are in the same order.
+                #
+                # End of line is platform dependent. Strip it off
+                expected_hierarchy = line.rstrip().split('\t')[5].split(',')
+                hierarchy = str(record).rstrip().split('\t')[5].split(',')
+                expected_hierarchy = dict([pair.split('=') for pair in expected_hierarchy])
+                hierarchy = dict([pair.split('=') for pair in hierarchy])
+                self.assertEqual(len(hierarchy), len(expected_hierarchy))
+                for key, value in hierarchy.items():
+                    self.assertEqual(value, expected_hierarchy[key])
         finally:
             f.close()        
 
@@ -56,13 +69,13 @@ def testRecord(self):
         self.assertEqual(record.residues.fragments, (('T','',''),('U','91','106')))
         self.assertEqual(record.sccs, 'b.1.2.1')
         self.assertEqual(record.sunid, 21953)
-        self.assertEqual(record.hierarchy, [['cl',48724],
-                                            ['cf',48725],
-                                            ['sf',49265],
-                                            ['fa',49266],
-                                            ['dm',49267],
-                                            ['sp',49268],
-                                            ['px',21953]])
+        self.assertEqual(record.hierarchy, {'cl' : 48724,
+                                            'cf' : 48725,
+                                            'sf' : 49265,
+                                            'fa' : 49266,
+                                            'dm' : 49267,
+                                            'sp' : 49268,
+                                            'px' : 21953})
 
     def testIndex(self):
         """Test CLA file indexing"""

Tests/test_SCOP_Scop.py

@@ -1,4 +1,5 @@
 # Copyright 2001 by Gavin E. Crooks.  All rights reserved.
+# Copyright 2010 Jeffrey Finkelstein
 # 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.
@@ -14,6 +15,25 @@
 
 class ScopTests(unittest.TestCase):
 
+    def _compare_cla_lines(self, cla_line_1, cla_line_2):
+        """ Compares the two specified Cla lines for equality.
+        
+        The order of the key-value pairs in the sixth field of the lines does
+        not matter. For more information, see
+        http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html
+        """
+        fields1 = cla_line_1.rstrip().split('\t')
+        fields2 = cla_line_2.rstrip().split('\t')
+        # the first five fields in a Cla line should be the same
+        for i in range(5):
+            if fields1[i] != fields2[i]:
+                return False
+        # get the hierarchy key-value pairs, which are unordered
+        hierarchy1 = set(fields1[5].split(','))
+        hierarchy2 = set(fields2[5].split(','))
+        if hierarchy1 != hierarchy2:
+            return False
+        return True
 
     def testParse(self):
 
@@ -35,7 +55,10 @@ def testParse(self):
 
         cla_out = StringIO()
         scop.write_cla(cla_out)
-        self.assertEqual(cla_out.getvalue(), cla)
+        for line, expected_line in zip(cla.rstrip().split('\n'), \
+                                           cla_out.getvalue().rstrip() \
+                                           .split('\n')):
+            self.assertTrue(self._compare_cla_lines(line, expected_line))
 
         des_out = StringIO()
         scop.write_des(des_out)