#!/usr/bin/env python from corebio import * from corebio.matrix import * from corebio.seq import * from corebio.utils import * from corebio import data from corebio._py3k import StringIO import unittest from numpy import * from test_corebio import * class test_AlphabeticArray(unittest.TestCase) : def test_create(self): matrix = AlphabeticArray( (protein_alphabet, protein_alphabet) ) matrix['A', 'C'] = 10 assert matrix[0,1]==10.0 class test_Motif(unittest.TestCase) : def test_read_transfac(self): f = testdata_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f.close() assert m[3, 'A']==0.0 assert m[0, 'G']==2.0 assert shape(m.array) == (12,4) f.close() f = testdata_stream("transfac_matrix2.txt") m = Motif.read_transfac(f) f.close() assert m[3, 'A']==3.0 assert m[0, 'G']==152.0 assert shape(m.array) == (15,4) # this one has extra Ps on start of each line f = testdata_stream("transfac_matrix3.txt") m = Motif.read_transfac(f) f.close() def test_reindex(self): f = testdata_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f.close() m2 = m.reindex("TCGA") assert( str(m2.alphabet) == "TCGA") for k in range(0, 12) : for i,a in enumerate("AGCT") : assert m[k,a] == m2[k,a] def test_reverse(self): f = testdata_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f2 = testdata_stream("transfac_matrix.txt") m2 = Motif.read_transfac(f2) m2.reverse() (K,N) = shape(m2) for k in range(0,K): for n in range(0,N): assert( m[k,n] == m2[K-k-1,n]) f.close() f2.close() def test_complement(self): f = testdata_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f2 = testdata_stream("transfac_matrix.txt") m2 = Motif.read_transfac(f2) m2.complement() (K,N) = shape(m2) for k in range(0,K): assert(m[k, 'A'] == m2[k, 'T']) assert(m[k, 'G'] == m2[k, 'C']) assert(m[k, 'C'] == m2[k, 'G']) assert(m[k, 'T'] == m2[k, 'A']) f.close() f2.close() def test_reverse_complement(self): f = testdata_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f2 = testdata_stream("transfac_matrix.txt") m2 = Motif.read_transfac(f2) m.complement() m.reverse() m2.reverse_complement() assert (m.array == m2.array).all() f.close() f2.close() class test_SubMatrix(unittest.TestCase) : def test_create(self): ab = 'ABCD' ar = asarray( [[1,2,3,4], [5,6,7,8],[9,10,11,12],[13,14,15,16]]) s = SubMatrix(ab, ar) assert s[0,0] == 1 assert s['A', 'A'] ==1 assert s['B', 'C'] ==7 s['B', 'C'] =-1 assert s['B', 'C'] ==-1 def test_get(self): ab = Alphabet('ABCD') ar = asarray( [[1,2,3,4], [5,6,7,8],[9,10,11,12],[13,14,15,16]]) s = SubMatrix(ab, ar) s1 = 'DCCBBBAAA' s2 = 'BA' v = s.index( (s1,s2) ) #print v for m,i in enumerate(s1) : for n,j in enumerate(s2) : assert s[i,j]== v[m,n] def test_get_subMatrix(self): ab = Alphabet('ABCD') ar = asarray( [[1,2,3,4], [5,6,7,8],[9,10,11,12],[13,14,15,16]]) mat = SubMatrix(ab, ar) mat2 = mat.reindex( 'ABC') assert all( mat2.array == asarray([[1,2,3], [5,6,7],[9,10,11]]) ) mat2 = mat.reindex( 'BA') assert all(mat2.array == asarray([[6,5],[2,1]]) ) mat2 = mat.reindex( Alphabet('BA')) assert all(mat2.array == asarray([[6,5],[2,1]]) ) def test_fail_get(self) : ab = Alphabet('ABCD') ar = asarray( [[1,2,3,4], [5,6,7,8],[9,10,11,12],[13,14,15,16]]) s = SubMatrix(ab, ar) self.assertRaises( IndexError, s.__getitem__ , ('E','A') ) self.assertRaises( IndexError, s.__getitem__ , ('5','6') ) #FIXME self.assertRaises( IndexError, s.index , ('E','A') ) def test_repr(self) : ab = Alphabet('ABCD') ar = asarray( [[1,2,3,4], [5,6,7,8],[9,10,11,12],[13,14,15,16]]) s = SubMatrix(ab, ar) string = repr(s) #print string def test_read(self) : f = StringIO(test_matrix1) mat = SubMatrix.read(f) assert mat['a','a'] ==4 def test_read_asymmetric_fail(self) : f = StringIO(test_matrix4) self.assertRaises(ValueError, SubMatrix.read, f ) def test_read_alphabets(self) : # incompatable alphabets f = StringIO(test_matrix3) self.assertRaises(ValueError, SubMatrix.read, f ) f = StringIO(test_matrix3) mat = SubMatrix.read(f, alphabet = Alphabet('ARNDCQEGHILKMFPSTWYV')) f2 = StringIO(test_matrix1) self.assertRaises(ValueError, SubMatrix.read, f2 , unambiguous_protein_alphabet) def test_read_corrupt(self) : f = StringIO(test_matrix2) self.assertRaises(ValueError, SubMatrix.read, f ) def test_read_pam(self): f = data.data_stream("pam250") mat = SubMatrix.read(f) self.assertEqual(mat[0,0], 2.0) f.close() f = data.data_stream("pam120") mat = SubMatrix.read(f) self.assertEqual(mat[4,5], -7) f.close() def test_read_blosum(self): f = data.data_stream("blosum80") mat = SubMatrix.read(f) self.assertEqual(mat[0,10], -3) f.close() f = data.data_stream("blosum62") mat = SubMatrix.read( f ) self.assertEqual(mat[4,5], -4) f.close() def test_read_blast(self): # New style blast matrices have letters at beginning of lines and a '*' f = testdata_stream("blosum35.blast.new") mat = SubMatrix.read(f ) self.assertEqual(mat[4,5], -3) f.close() # Matrices formatted for old blast have a '*' (stop) # column and no letters at the beggining of lines f = testdata_stream("blosum35.blast") mat = SubMatrix.read(f ) self.assertEqual(mat[0,10], -2) self.assertEqual(mat.array.shape, (23,23)) f.close() # For comparison, we'll also parse a matrix without '*' f = testdata_stream("pam250.mat") mat = SubMatrix.read(f) self.assertEqual(mat[4,5], -5) f.close() test_matrix1 = """# A Test Matrix # More comments # And blank line should be ignored A 4 -2 -2 -2 0 -1 -1 -1 -2 -2 -2 -2 -1 -2 -1 0 -1 -3 -2 -1 -2 -1 -1 R -2 6 -1 -1 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -2 -2 -3 3 -1 -1 N -2 -1 7 1 -3 0 0 -1 0 -5 -4 0 -3 -4 -2 0 -1 -3 -2 -4 3 -1 -1 D -2 -1 1 7 -4 0 1 -1 -1 -6 -5 0 -4 -5 -1 0 -1 -4 -3 -5 0 -2 -2 C 0 -4 -3 -4 12 -3 -4 -3 -3 -1 -2 -4 -1 -2 -3 -2 -1 -2 -2 0 -3 5 -2 Q -1 1 0 0 -3 6 1 -2 0 -3 -3 1 -2 -3 -1 0 -1 -2 -2 -3 0 1 -1 E -1 0 0 1 -4 1 5 -2 -1 -4 -4 1 -3 -4 -1 -1 -1 -3 -3 -4 0 -1 -1 G -1 -3 -1 -1 -3 -2 -2 7 -2 -6 -5 -2 -4 -5 -2 -1 -2 -4 -4 -5 -2 -2 -2 H -2 0 0 -1 -3 0 -1 -2 9 -3 -3 -1 -2 -1 -2 -1 -1 0 0 -3 0 -1 -1 I -2 -3 -5 -6 -1 -3 -4 -6 -3 5 2 -4 1 0 -4 -4 -2 -1 -1 3 -4 -2 -2 L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 5 -3 2 1 -3 -3 -2 -1 -1 1 -4 -2 -2 K -2 2 0 0 -4 1 1 -2 -1 -4 -3 5 -2 -4 -1 -1 -1 -3 -3 -3 1 -1 -1 M -1 -2 -3 -4 -1 -2 -3 -4 -2 1 2 -2 7 1 -3 -2 -1 0 0 1 -3 -2 -1 F -2 -3 -4 -5 -2 -3 -4 -5 -1 0 1 -4 1 7 -3 -3 -2 3 3 0 -3 -2 -1 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -4 -3 -1 -3 -3 8 -1 -2 -3 -3 -3 -2 -2 -2 S 0 -1 0 0 -2 0 -1 -1 -1 -4 -3 -1 -2 -3 -1 4 1 -3 -2 -3 0 -1 -1 T -1 -1 -1 -1 -1 -1 -1 -2 -1 -2 -2 -1 -1 -2 -2 1 5 -2 -2 -1 -1 -1 -1 W -3 -2 -3 -4 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -3 -2 12 3 -2 -3 -2 -1 Y -2 -2 -2 -3 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -2 -2 3 8 -2 -2 -2 -1 V -1 -3 -4 -5 0 -3 -4 -5 -3 3 1 -3 1 0 -3 -3 -1 -2 -2 5 -4 -2 -2 B -2 3 3 0 -3 0 0 -2 0 -4 -4 1 -3 -3 -2 0 -1 -3 -2 -4 3 -1 -1 Z -1 -1 -1 -2 5 1 -1 -2 -1 -2 -2 -1 -2 -2 -2 -1 -1 -2 -2 -2 -1 3 -1 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -2 -1 -1 -1 -2 -1 -1 -1 -1 -2 -1 -1 -1 """ test_matrix2 = """# An invalid Test Matrix # Its got a non-numerical value in it. Is the correct exception raised? # And blank line should be ignored A 4 -2 -2 -2 0 -1 -1 -1 -2 -2 -2 -2 -1 -2 -1 0 -1 -3 -2 -1 -2 -1 -1 R -2 6 -1 -1 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -2 -2 -3 3 -1 -1 N -2 -1 7 1 -3 0 0 -1 0 -5 -4 0 -3 -4 -2 0 -1 -3 -2 -4 3 -1 -1 D -2 -1 1 7 -4 0 1 -1 -1 -6 -5 0 -4 -5 -1 0 -1 -4 -3 -5 0 -2 -2 C 0 -4 -3 -4 12 -3 -4 -3 -3 -1 -2 -4 -1 -2 -3 -2 -1 -2 -2 0 -3 5 -2 Q -1 1 0 0 -3 6 1 -2 0 -3 -3 1 -2 -3 -1 0 -1 -2 -2 -3 0 1 -1 E -1 0 0 1 -4 x 5 -2 -1 -4 -4 1 -3 -4 -1 -1 -1 -3 -3 -4 0 -1 -1 G -1 -3 -1 -1 -3 -2 -2 7 -2 -6 -5 -2 -4 -5 -2 -1 -2 -4 -4 -5 -2 -2 -2 H -2 0 0 -1 -3 0 -1 -2 9 -3 -3 -1 -2 -1 -2 -1 -1 0 0 -3 0 -1 -1 I -2 -3 -5 -6 -1 -3 -4 -6 -3 5 2 -4 1 0 -4 -4 -2 -1 -1 3 -4 -2 -2 L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 5 -3 2 1 -3 -3 -2 -1 -1 1 -4 -2 -2 K -2 2 0 0 -4 1 1 -2 -1 -4 -3 5 -2 -4 -1 -1 -1 -3 -3 -3 1 -1 -1 M -1 -2 -3 -4 -1 -2 -3 -4 -2 1 2 -2 7 1 -3 -2 -1 0 0 1 -3 -2 -1 F -2 -3 -4 -5 -2 -3 -4 -5 -1 0 1 -4 1 7 -3 -3 -2 3 3 0 -3 -2 -1 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -4 -3 -1 -3 -3 8 -1 -2 -3 -3 -3 -2 -2 -2 S 0 -1 0 0 -2 0 -1 -1 -1 -4 -3 -1 -2 -3 -1 4 1 -3 -2 -3 0 -1 -1 T -1 -1 -1 -1 -1 -1 -1 -2 -1 -2 -2 -1 -1 -2 -2 1 5 -2 -2 -1 -1 -1 -1 W -3 -2 -3 -4 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -3 -2 12 3 -2 -3 -2 -1 Y -2 -2 -2 -3 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -2 -2 3 8 -2 -2 -2 -1 V -1 -3 -4 -5 0 -3 -4 -5 -3 3 1 -3 1 0 -3 -3 -1 -2 -2 5 -4 -2 -2 B -2 3 3 0 -3 0 0 -2 0 -4 -4 1 -3 -3 -2 0 -1 -3 -2 -4 3 -1 -1 Z -1 -1 -1 -2 5 1 -1 -2 -1 -2 -2 -1 -2 -2 -2 -1 -1 -2 -2 -2 -1 3 -1 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -2 -1 -1 -1 -2 -1 -1 -1 -1 -2 -1 -1 -1 """ test_matrix3 = """# # This test matrix has a smaller alphabet A 4 -2 -2 -2 0 -1 -1 -1 -2 -2 -2 -2 -1 -2 -1 0 -1 -3 -2 -1 R -2 6 -1 -1 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -2 -2 -3 N -2 -1 7 1 -3 0 0 -1 0 -5 -4 0 -3 -4 -2 0 -1 -3 -2 -4 D -2 -1 1 7 -4 0 1 -1 -1 -6 -5 0 -4 -5 -1 0 -1 -4 -3 -5 C 0 -4 -3 -4 12 -3 -4 -3 -3 -1 -2 -4 -1 -2 -3 -2 -1 -2 -2 0 Q -1 1 0 0 -3 6 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -2 -2 -3 E -1 0 0 1 -4 4 5 -2 -1 -4 -4 1 -3 -4 -1 -1 -1 -3 -3 -4 G -1 -3 -1 -1 -3 -2 -2 7 -2 -6 -5 -2 -4 -5 -2 -1 -2 -4 -4 -5 H -2 0 0 -1 -3 0 -1 -2 9 -3 -3 -1 -2 -1 -2 -1 -1 0 0 -3 I -2 -3 -5 -6 -1 -3 -4 -6 -3 5 2 -4 1 0 -4 -4 -2 -1 -1 3 L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 5 -3 2 1 -3 -3 -2 -1 -1 1 K -2 2 0 0 -4 1 1 -2 -1 -4 -3 5 -2 -4 -1 -1 -1 -3 -3 -3 M -1 -2 -3 -4 -1 -2 -3 -4 -2 1 2 -2 7 1 -3 -2 -1 0 0 1 F -2 -3 -4 -5 -2 -3 -4 -5 -1 0 1 -4 1 7 -3 -3 -2 3 3 0 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -4 -3 -1 -3 -3 8 -1 -2 -3 -3 -3 S 0 -1 0 0 -2 0 -1 -1 -1 -4 -3 -1 -2 -3 -1 4 1 -3 -2 -3 T -1 -1 -1 -1 -1 -1 -1 -2 -1 -2 -2 -1 -1 -2 -2 1 5 -2 -2 -1 W -3 -2 -3 -4 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -3 -2 12 3 -2 Y -2 -2 -2 -3 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -2 -2 3 8 -2 V -1 -3 -4 -5 0 -3 -4 -5 -3 3 1 -3 1 0 -3 -3 -1 -2 -2 5 """ test_matrix4 = """# This matrix is invalid because it is asymetric! (AR, RA) A 4 2 -2 -2 0 -1 -1 -1 -2 -2 -2 -2 -1 -2 -1 0 -1 -3 -2 -1 -2 -1 -1 R -2 6 -1 -1 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -2 -2 -3 3 -1 -1 N -2 -1 7 1 -3 0 0 -1 0 -5 -4 0 -3 -4 -2 0 -1 -3 -2 -4 3 -1 -1 D -2 -1 1 7 -4 0 1 -1 -1 -6 -5 0 -4 -5 -1 0 -1 -4 -3 -5 0 -2 -2 C 0 -4 -3 -4 12 -3 -4 -3 -3 -1 -2 -4 -1 -2 -3 -2 -1 -2 -2 0 -3 5 -2 Q -1 1 0 0 -3 6 1 -2 0 -3 -3 1 -2 -3 -1 0 -1 -2 -2 -3 0 1 -1 E -1 0 0 1 -4 1 5 -2 -1 -4 -4 1 -3 -4 -1 -1 -1 -3 -3 -4 0 -1 -1 G -1 -3 -1 -1 -3 -2 -2 7 -2 -6 -5 -2 -4 -5 -2 -1 -2 -4 -4 -5 -2 -2 -2 H -2 0 0 -1 -3 0 -1 -2 9 -3 -3 -1 -2 -1 -2 -1 -1 0 0 -3 0 -1 -1 I -2 -3 -5 -6 -1 -3 -4 -6 -3 5 2 -4 1 0 -4 -4 -2 -1 -1 3 -4 -2 -2 L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 5 -3 2 1 -3 -3 -2 -1 -1 1 -4 -2 -2 K -2 2 0 0 -4 1 1 -2 -1 -4 -3 5 -2 -4 -1 -1 -1 -3 -3 -3 1 -1 -1 M -1 -2 -3 -4 -1 -2 -3 -4 -2 1 2 -2 7 1 -3 -2 -1 0 0 1 -3 -2 -1 F -2 -3 -4 -5 -2 -3 -4 -5 -1 0 1 -4 1 7 -3 -3 -2 3 3 0 -3 -2 -1 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -4 -3 -1 -3 -3 8 -1 -2 -3 -3 -3 -2 -2 -2 S 0 -1 0 0 -2 0 -1 -1 -1 -4 -3 -1 -2 -3 -1 4 1 -3 -2 -3 0 -1 -1 T -1 -1 -1 -1 -1 -1 -1 -2 -1 -2 -2 -1 -1 -2 -2 1 5 -2 -2 -1 -1 -1 -1 W -3 -2 -3 -4 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -3 -2 12 3 -2 -3 -2 -1 Y -2 -2 -2 -3 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -2 -2 3 8 -2 -2 -2 -1 V -1 -3 -4 -5 0 -3 -4 -5 -3 3 1 -3 1 0 -3 -3 -1 -2 -2 5 -4 -2 -2 B -2 3 3 0 -3 0 0 -2 0 -4 -4 1 -3 -3 -2 0 -1 -3 -2 -4 3 -1 -1 Z -1 -1 -1 -2 5 1 -1 -2 -1 -2 -2 -1 -2 -2 -2 -1 -1 -2 -2 -2 -1 3 -1 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -2 -1 -1 -1 -2 -1 -1 -1 -1 -2 -1 -1 -1 """ if __name__ == '__main__': unittest.main()