def test_wuss_to_vienna(self):
"""wuss_to_vienna() should transform Wuss into Vienna"""
empty = WussStructure('.....')
normal = WussStructure('[.{[<...}}}}')
pseudo = WussStructure('[..AA..]..aa')
self.assertEqual(wuss_to_vienna(normal), '(.(((...))))')
self.assertEqual(wuss_to_vienna(empty), '.....')
self.assertEqual(wuss_to_vienna(pseudo), '(......)....')
def test_wuss_to_vienna(self):
"""wuss_to_vienna() should transform Wuss into Vienna"""
empty = WussStructure('.....')
normal = WussStructure('[.{[<...}}}}')
pseudo = WussStructure('[..AA..]..aa')
self.assertEqual(wuss_to_vienna(normal),'(.(((...))))')
self.assertEqual(wuss_to_vienna(empty),'.....')
self.assertEqual(wuss_to_vienna(pseudo),'(......)....')
def CMfinderParser(lines):
"""Parser for CMfinder output format
Parser tested through RfamParser test
"""
for info, alignment, struct in RfamParser(lines,strict=False):
struct = wuss_to_vienna(struct)
pairs = struct.toPairs()
return [alignment, pairs]
def CMfinderParser(lines):
"""Parser for CMfinder output format
Parser tested through RfamParser test
"""
for info, alignment, struct in RfamParser(lines,strict=False):
struct = wuss_to_vienna(struct)
pairs = struct.toPairs()
return [alignment, pairs]
def test_cmalign_from_alignment(self):
"""cmalign_from_alignment should work as expected.
"""
#Align with cmalign_from_alignment without original alignment.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,include_aln=False)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#should work with gapped seqs. Need to test this is taken care of
# since cmalign segfaults when there are gaps in the seqs to be aligned.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should work with ungapped seqs.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should return standard out
aln, struct,stdout = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,\
return_stdout=True)
#Test that standard out is same length as expected
self.assertEqual(len(stdout.split('\n')),\
len(CMALIGN_STDOUT.split('\n')))
def test_cmalign_from_alignment(self):
"""cmalign_from_alignment should work as expected.
"""
#Align with cmalign_from_alignment without original alignment.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,include_aln=False)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#should work with gapped seqs. Need to test this is taken care of
# since cmalign segfaults when there are gaps in the seqs to be aligned.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should work with ungapped seqs.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should return standard out
aln, struct,stdout = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,\
return_stdout=True)
#Test that standard out is same length as expected
self.assertEqual(len(stdout.split('\n')),\
len(CMALIGN_STDOUT.split('\n')))
def test_cmalign_from_file(self):
"""cmalign_from_file should work as expected.
"""
#Align with cmalign_from_file without original alignment.
aln,struct = cmalign_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,\
moltype=RNA)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#Align with cmalign_from_file using original alignment.
aln,struct = cmalign_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,\
moltype=RNA,\
alignment_file_path=self.aln2_file,\
include_aln=True)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
def test_cmalign_from_file(self):
"""cmalign_from_file should work as expected.
"""
#Align with cmalign_from_file without original alignment.
aln,struct = cmalign_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,\
moltype=RNA)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#Align with cmalign_from_file using original alignment.
aln,struct = cmalign_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,\
moltype=RNA,\
alignment_file_path=self.aln2_file,\
include_aln=True)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
