def testStr(self):
     """Test if we can convert each record to a string correctly"""
     f = open(self.filename)
     try:
         for line in f:
             record = Cla.Record(line)
             # 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(',')
             expected_hierarchy = dict(
                 pair.split('=') for pair in expected_hierarchy)
             actual_hierarchy = str(record).rstrip().split('\t')[5].split(
                 ',')
             actual_hierarchy = dict(
                 pair.split('=') for pair in actual_hierarchy)
             self.assertEqual(len(actual_hierarchy),
                              len(expected_hierarchy))
             for key, actual_value in actual_hierarchy.iteritems():
                 self.assertEqual(actual_value, expected_hierarchy[key])
     finally:
         f.close()
Example #2
0
 def testParse(self):
     """Test if all records in a CLA file are being read."""
     count = 0
     with open(self.filename) as f:
         records = Cla.parse(f)
         for record in records:
             count += 1
     self.assertEqual(count, 14)
Example #3
0
    def testIndex(self) :
        index = Cla.Index(self.filename)
        
        assert len(index)==14
        assert index.has_key('d4hbia_')

        rec = index['d1hbia_']
        assert rec.sunid == 14996
Example #4
0
    def testError(self) :
        corruptRec = "49268\tsp\tb.1.2.1\t-\n"

        try:
            record = Cla.Record(corruptRec)
            assert False, "Should never get here"
        except ValueError, e :
            pass
Example #5
0
    def testIndex(self):
        """Test CLA file indexing."""
        index = Cla.Index(self.filename)

        self.assertEqual(len(index), 14)
        self.assertIn("d4hbia_", index)

        rec = index["d1hbia_"]
        self.assertEqual(rec.sunid, 14996)
    def testIndex(self):
        """Test CLA file indexing"""
        index = Cla.Index(self.filename)

        self.assertEqual(len(index), 14)
        self.assertTrue('d4hbia_' in index)

        rec = index['d1hbia_']
        self.assertEqual(rec.sunid, 14996)
Example #7
0
 def testStr(self):
     f = open(self.filename)
     try: 
         for line in f:
             record = Cla.Record(line)
             #End of line is platform dependent. Strip it off
             assert str(record).rstrip() == line.rstrip()
     finally:
         f.close()        
Example #8
0
 def testParse(self):
     """Test if all records in a CLA file are being read"""
     f=open(self.filename)
     try:
         count = 0
         records = Cla.parse(f)
         for record in records:
             count +=1
         self.assertEqual(count, 14)
     finally:
         f.close()
Example #9
0
 def testParse(self):
     """Can we parse a CLA file?"""
     f=open(self.filename)
     try: 
         count = 0
         records = Cla.parse(f)
         for record in records:
             count +=1
         assert count == 14, "Wrong number of records?!"
     finally:
         f.close()
 def testParse(self):
     """Test if all records in a CLA file are being read"""
     f = open(self.filename)
     try:
         count = 0
         records = Cla.parse(f)
         for record in records:
             count += 1
         self.assertEqual(count, 14)
     finally:
         f.close()
Example #11
0
 def testParse(self):
     """Can we parse a CLA file?"""
     f=open(self.filename)
     try: 
         count = 0
         records = Cla.parse(f)
         for record in records:
             count +=1
         assert count == 14, "Wrong number of records?!"
     finally:
         f.close()
Example #12
0
    def testRecord(self) :
        recLine = 'd1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953'

        record = Cla.Record(recLine)
        assert record.sid =='d1dan.1'
        assert record.residues.pdbid =='1dan'
        assert record.residues.fragments ==(('T','',''),('U','91','106'))
        assert record.sccs == 'b.1.2.1'
        assert record.sunid == 21953
        assert record.hierarchy == [['cl',48724],['cf',48725],['sf',49265],
             ['fa',49266],['dm',49267],['sp',49268],
             ['px',21953]], record.hierarchy
Example #13
0
    def testRecord(self):
        """Test one record in detail"""
        recLine = 'd1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953'

        record = Cla.Record(recLine)
        self.assertEqual(record.sid, 'd1dan.1')
        self.assertEqual(record.residues.pdbid, '1dan')
        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})
Example #14
0
    def testRecord(self):
        """Test one record in detail."""
        recLine = "d1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953"

        record = Cla.Record(recLine)
        self.assertEqual(record.sid, "d1dan.1")
        self.assertEqual(record.residues.pdbid, "1dan")
        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
            })
Example #15
0
def main():
    try:
        opts, args = getopt.getopt(
            sys.argv[1:], "hp:o:i:",
            ["help", "usage", "pdb=", "output=", "input="])
    except getopt.GetoptError:
        # show help information and exit:
        usage()
        sys.exit(2)

    input = None
    in_handle = None
    output = None
    pdb_url = None
    cla_url = None
    raf_url = None

    for o, a in opts:
        if o in ("-h", "--help", "--usage"):
            usage()
            sys.exit()
        elif o in ("-o", "--output"):
            output = a
        elif o in ("-i", "--input"):
            input = a
        elif o in ("-p", "--pdb"):
            pdb_url = a

    if len(args) < 2:
        sys.stderr.write(
            "Not enough arguments. Try --help for more details.\n")
        sys.exit(2)

    raf_url = args[0]
    cla_url = args[1]

    (raf_filename, headers) = _urlretrieve(raf_url)
    seqMapIndex = Raf.SeqMapIndex(raf_filename)

    (cla_filename, headers) = _urlretrieve(cla_url)
    claIndex = Cla.Index(cla_filename)

    if input is None:
        sids = args[2:]
    elif input == '-':
        sids = sys.stdin
    else:
        in_handle = open(input)
        sids = in_handle

    try:
        for sid in sids:
            if not sid or sid[0:1] == '#':
                continue
            id = sid[0:7]
            pdbid = id[1:5]
            s = pdbid[0:1]
            if s == '0' or s == 's':
                sys.stderr.write("No coordinates for domain %s\n" % id)
                continue

            if output is None:
                filename = id + ".ent"
                out_handle = open(filename, "w+")
            elif output == '-':
                out_handle = sys.stdout
            else:
                out_handle = open(output, "w+")

            try:
                try:
                    claRec = claIndex[id]
                    residues = claRec.residues
                    seqMap = seqMapIndex.getSeqMap(residues)
                    pdbid = residues.pdbid

                    f = open_pdb(pdbid, pdb_url)
                    try:
                        seqMap.getAtoms(f, out_handle)
                    finally:
                        f.close()
                except (IOError, KeyError, RuntimeError) as e:
                    sys.stderr.write("I cannot do SCOP domain %s : %s\n" %
                                     (id, e))
            finally:
                out_handle.close()
    finally:
        if in_handle is not None:
            in_handle.close()