added slice operator to SequenceHandle

Also, added unit tests for slice operators of SequenceList,
SequenceHandle and AlignmentHandle exports. Fixes BZDNG-249.

modules/seq/base/pymod/export_sequence.cc

@@ -57,11 +57,17 @@ T do_slice(const T& t, slice& sl) {
   int start=0, end=t.GetCount();
   try {
     start=extract<int>(sl.start());
+    if (start<0) {
+      start=t.GetCount()+start;
+    }    
   } catch(error_already_set) {
     PyErr_Clear();
   }
   try {
     end=extract<int>(sl.stop());
+    if (end<0) {
+      end=t.GetCount()+end;
+    }    
   } catch(error_already_set) {
     PyErr_Clear();
   }
@@ -78,16 +84,43 @@ SequenceList do_slice_b(SequenceList& t, slice sl)
   return do_slice<SequenceList>(t, sl);
 }
 
+String slice_seq(const ConstSequenceHandle& sh, slice& sl) {
+  int start=0, end=sh.GetLength();
+  try {
+    start=extract<int>(sl.start());
+    if (start<0) {
+      start=sh.GetLength()+start;
+    }    
+  } catch(error_already_set) {
+    PyErr_Clear();
+  }
+  try {
+    end=extract<int>(sl.stop());
+    if (end<0) {
+      end=sh.GetLength()+end;
+    }
+  } catch(error_already_set) {
+    PyErr_Clear();
+  }
+  String s=sh.GetString();
+  return s.substr(start, end-start);
+}
 
 AlignedRegion slice_aln(const AlignmentHandle& aln, slice sl) {
   int start=0, end=aln.GetLength();
   try {
     start=extract<int>(sl.start());
+    if (start<0) {
+      start=aln.GetLength()+start;
+    }    
   } catch(error_already_set) {
     PyErr_Clear();
   }
   try {
     end=extract<int>(sl.stop());
+    if (end<0) {
+      end=aln.GetLength()+end;
+    }
   } catch(error_already_set) {
     PyErr_Clear();
   }
@@ -212,6 +245,7 @@ void const_seq_handle_def(O& bp_class)
     .def("GetOneLetterCode", &C::GetOneLetterCode)
     .def("__iter__", iterator<C>())
     .def("__getitem__", &C::GetOneLetterCode)
+    .def("__getitem__", slice_seq)
     .def("GetOffset", &C::GetOffset)
     .def("Copy", &C::Copy)
     .def("IsValid", &C::IsValid)

modules/seq/base/tests/test_seq.py

@@ -20,6 +20,55 @@ class TestSeq(unittest.TestCase):
   def setUp(self):
     self.ent=fixture()
     
+  def testSeqSlice(self):
+    seq_string='abcdefg'
+    s=seq.CreateSequence('A', seq_string)
+    self.assertEqual(s[1:5], seq_string[1:5])
+    self.assertEqual(s[:-1], seq_string[:-1])
+    self.assertEqual(s[-3:-2], seq_string[-3:-2])
+    self.assertEqual(s[-3:], seq_string[-3:])
+    self.assertEqual(s[3:4], seq_string[3:4])
+    
+  def testSeqListSlice(self):
+    a=seq.CreateSequence('A','aaaa')
+    b=seq.CreateSequence('B','bbbb')
+    c=seq.CreateSequence('C','cccc')
+    d=seq.CreateSequence('D','dddd')
+    sl=seq.CreateSequenceList(a, b, c, d)
+    sliced=sl[1:]
+    self.assertEqual(len(sliced), 3)
+    self.assertEqual(str(sliced[0]), str(b))
+    self.assertEqual(str(sliced[1]), str(c))
+    self.assertEqual(str(sliced[2]), str(d))
+    sliced=sl[:-1]
+    self.assertEqual(len(sliced), 3)
+    self.assertEqual(str(sliced[0]), str(a))
+    self.assertEqual(str(sliced[1]), str(b))
+    self.assertEqual(str(sliced[2]), str(c))
+    sliced=sl[-1:]
+    self.assertEqual(len(sliced), 1)
+    self.assertEqual(str(sliced[0]), str(d))
+    
+  def testAlnSlice(self):
+    a=seq.CreateSequence('A','abcd')
+    b=seq.CreateSequence('B','efgh')
+    c=seq.CreateSequence('C','ijkl')
+    d=seq.CreateSequence('D','mnop')
+    aln=seq.CreateAlignment(a, b, c, d)
+    sliced=aln[1:]
+    self.assertEqual(len(sliced), 3)
+    self.assertEqual(str(sliced[0]), 'bfjn')
+    self.assertEqual(str(sliced[1]), 'cgko')
+    self.assertEqual(str(sliced[2]), 'dhlp')
+    sliced=aln[:-1]
+    self.assertEqual(len(sliced), 3)
+    self.assertEqual(str(sliced[0]), 'aeim')
+    self.assertEqual(str(sliced[1]), 'bfjn')
+    self.assertEqual(str(sliced[2]), 'cgko')
+    sliced=aln[-1:]
+    self.assertEqual(len(sliced), 1)
+    self.assertEqual(str(sliced[0]), 'dhlp')
+
   def testViewsFromSequences_01(self):
     seq_a=seq.CreateSequence("A", "ABCD-FGH")
     seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))