#!/usr/bin/env python
 
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from corebio import *
from corebio.seq import *
from corebio.seq_io import *
from corebio.seq_io import msf_io
from test_corebio import *

from corebio._py3k import StringIO

import unittest

class test_msf_io(unittest.TestCase) :

    def test_parse_msf(self) :
        f = testdata_stream("dna.msf")
        seqs = msf_io.read(f)
        self.assertEqual(len(seqs), 10)
        self.assertEqual(seqs[1].name, "Carp")
        self.assertEqual(len(seqs[1]), 705)
        self.assertEqual( str(seqs[2][0:10]), 'ATGGCCAACC')
        f.close()
        
    def test_parse_msf2(self) :
        f = testdata_stream("cox2.msf")
        seqs = msf_io.read(f)
        self.assertEqual(len(seqs), 5)
        self.assertEqual(seqs[1].name, "cox2_crifa")
        self.assertEqual(len(seqs[1]), 166)
        self.assertEqual( str(seqs[2][0:10]), 'MSFILTFWMI')
        f.close()
           
    def test_parse_1beo(self) :
        f = testdata_stream("1beo.msf")
        seqs = msf_io.read(f) 
        f.close()
   
        
    """ Wrong alphabet should throw a parsing error """
    def test_parse_error(self) :
        f = testdata_stream("cox2.msf")
        self.assertRaises(ValueError, 
            msf_io.read, f, nucleic_alphabet )
        f.close()
            
    def test_parse_fasta_fail2(self) :
        # should fail with parse error
        f = testdata_stream("globin.fa")
        self.assertRaises(ValueError, 
            msf_io.read, f )
        f.close()
            
    def test_parse_plain_fail(self) :
        # should fail with parse error
        f = StringIO(plain_io.example)
        self.assertRaises(ValueError, 
            msf_io.read, f  )
        f.close()
            
    
    def test_parse_phylip_fail(self) :
        # should fail with parse error
        f = testdata_stream("phylip_test_2.phy")
        self.assertRaises(ValueError, 
            msf_io.read, f )
        f.close()
                                                 
if __name__ == '__main__':
    unittest.main()
