#!/usr/bin/env python
 
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#  Lawrence Berkeley National Laboratory (subject to receipt of any required
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import unittest

from corebio import *
from corebio.seq import *
from corebio.seq_io import *
from corebio.seq_io import stockholm_io
from corebio._py3k import StringIO

from test_corebio import *


class test_stockholm_io(unittest.TestCase) :

    def test_parse1(self) :
        with testdata_stream("pfam.txt") as f:
            seqs = stockholm_io.read(f)
        #self.assertEqual(len(seqs), 7)
        self.assertEqual(seqs[1].name, "O61132/1-232")
        self.assertEqual(len(seqs[1]), 265)
  
    def test_parse2(self) :
        f= StringIO(stockholm_io.example)
        seqs = stockholm_io.read(f)
        self.assertEqual(len(seqs), 5)
        self.assertEqual(seqs[1].name, "O83071/259-312")
        self.assertEqual(len(seqs[1]), 43)
  
#12345678901234567890123456789012345678901234567890
#12*50 +6 = 606
#QYVTVFYGVPAWRNATIPLFCATKNR.......DTWGTTQCLPDNDDYSE
  
  
    def test_parse3(self) :
        with testdata_stream("pfam_example.txt") as f:
            seqs = stockholm_io.read(f)
        self.assertEqual(len(seqs), 24)
        self.assertEqual(seqs[5].name, "ENV_HV2BE/24-510")
        self.assertEqual(len(seqs[1]), 606)
        self.assertEqual( str(seqs[0][-6:]) , 'TSRNKR')
  
  
    def test_parse_error(self) :
        """ Wrong alphabet should throw a parsing error """
        f = StringIO(stockholm_io.example)
        self.assertRaises(ValueError, 
            clustal_io.read, f, nucleic_alphabet )

    def test_parse_fasta_fail(self) :
        # should fail with parse error
        f = StringIO(fasta_io.example)
        self.assertRaises(ValueError, 
            stockholm_io.read, f , protein_alphabet )
        
    def test_parse_fasta_fail2(self) :
        # should fail with parse error
        with testdata_stream("globin.fa") as f:
            self.assertRaises(ValueError, stockholm_io.read, f )


    def test_parse_fail(self) :
        # should fail with parse error
        examples = (
            StringIO(clustal_io.example),
        )
        
        for f in examples :
            self.assertRaises(ValueError, 
                stockholm_io.read, f )

             
if __name__ == '__main__':
    unittest.main()