Python clustal_from_alignment Examples

Example #1

File: test_clustal.py Project: carze/clovr-base

 def test_clustal_from_alignment(self):
     """should return correct clustal string."""
     self.assertEqual(clustal_from_alignment({}),'')
     self.assertEqual(clustal_from_alignment(self.alignment_dict),\
         self.clustal_with_label)
     self.assertEqual(clustal_from_alignment(self.alignment_dict,
             interleave_len=2),self.clustal_with_label_lw2)

Example #2

 def test_clustal_from_alignment_reordered(self):
     """should return correct clustal string."""
     self.assertEqual(clustal_from_alignment(self.alignment_object),\
         self.clustal_with_label_reordered)
     self.assertEqual(
         clustal_from_alignment(self.alignment_object, interleave_len=2),
         self.clustal_with_label_lw2_reordered)

Example #3

 def test_clustal_from_alignment(self):
     """should return correct clustal string."""
     self.assertEqual(clustal_from_alignment({}),'')
     self.assertEqual(clustal_from_alignment(self.alignment_dict),\
         self.clustal_with_label)
     self.assertEqual(clustal_from_alignment(self.alignment_dict,
             interleave_len=2),self.clustal_with_label_lw2)

Example #4

File: rnaalifold.py Project: cxhernandez/pycogent

def rnaalifold_from_alignment(aln,moltype=RNA,params=None):
    """Returns seq, pairs, folding energy for alignment.
    """
    #Create Alignment object.  Object will handle if seqs are unaligned.
    aln = Alignment(aln,MolType=RNA)
    int_map, int_keys = aln.getIntMap()

    app = RNAalifold(WorkingDir='/tmp',\
        InputHandler='_input_as_multiline_string',params=params)
    res = app(clustal_from_alignment(int_map))
    
    #seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines())
    pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines())

    res.cleanUp()
    return pairs_list

Example #5

File: rnaalifold.py Project: mikerobeson/pycogent

def rnaalifold_from_alignment(aln, moltype=RNA, params=None):
    """Returns seq, pairs, folding energy for alignment.
    """
    #Create Alignment object.  Object will handle if seqs are unaligned.
    aln = Alignment(aln, MolType=RNA)
    int_map, int_keys = aln.getIntMap()

    app = RNAalifold(WorkingDir='/tmp',\
        InputHandler='_input_as_multiline_string',params=params)
    res = app(clustal_from_alignment(int_map))

    #seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines())
    pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines())

    res.cleanUp()
    return pairs_list

Example #6

File: test_clustal.py Project: carze/clovr-base

 def test_clustal_from_alignment_reordered(self):
     """should return correct clustal string."""
     self.assertEqual(clustal_from_alignment(self.alignment_object),\
         self.clustal_with_label_reordered)
     self.assertEqual(clustal_from_alignment(self.alignment_object,
             interleave_len=2),self.clustal_with_label_lw2_reordered)