#!/usr/bin/env python
 
#  Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
#  This software is distributed under the MIT Open Source License.
#  <http://www.opensource.org/licenses/mit-license.html>
#
#  Permission is hereby granted, free of charge, to any person obtaining a 
#  copy of this software and associated documentation files (the "Software"),
#  to deal in the Software without restriction, including without limitation
#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
#  and/or sell copies of the Software, and to permit persons to whom the
#  Software is furnished to do so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included
#  in all copies or substantial portions of the Software.
#
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
#  THE SOFTWARE.
#


from corebio import *
from corebio.seq import *
from corebio.seq_io import *
from test_corebio import *

from StringIO import StringIO

import corebio.seq_io.intelligenetics_io as ig_io

import unittest
import time
import sys

class test_ig_io(unittest.TestCase) :

    def test_read(self) :
        f = StringIO(ig_io.example)
        seqs = ig_io.read(f)
  
        self.assertEquals(len(seqs), 2)        
        self.assertEquals(seqs[0].description, "H.sapiens fau mRNA, 518 bases")
        self.assertEquals(seqs[1].name, "HSFAU1")
        self.assertEquals(len(seqs[1]), 299)

    def test_read2(self):
        f = testdata_stream("intelligenetics.txt")
        seqs = ig_io.read(f)
        self.assertEquals(len(seqs[0]), 518)
        self.assertEquals(len(seqs[1]), 2016)
       
    def test_write_seq(self) :
        f = StringIO(ig_io.example)
        seqs = ig_io.read(f)
        
        fout = StringIO()
        ig_io.write(fout,seqs)
        
        fout.seek(0)

        seqs2 = ig_io.read(fout)
        
        self.assertEquals(seqs, seqs2)
    
   
   
          
        
if __name__ == '__main__':
    unittest.main()