1 """Parsing of GO annotation of TigrGeneIndices's TC sequence --yong27, 2005-05-03
   2 """
   3 import sys, unittest
   4 
   5 class Go:
   6     def __init__(self, aRecordLine):
   7         words = aRecordLine.split()
   8         self.id = words[0].split(':')[1]
   9         self.proof = words[-1]
  10         self.category = words[-2]
  11         self.description = ' '.join(words[1:-2])
  12 
  13 class TcGo:
  14     def __init__(self, aTcId):
  15         self.id = aTcId
  16         self.gos = dict()
  17 
  18     def addGo(self, aGo):
  19         self.gos[aGo.id] = aGo
  20 
  21     def getGo(self, aGoId):
  22         return self.gos.get(aGoId)
  23 
  24 class TcGoGenerator:
  25     def __init__(self, aFile):
  26         self.file = aFile
  27         self.g = self.parse()
  28 
  29     def parse(self):
  30         strRecord = list()
  31         for line in self.file:
  32             if line[0]=='>' and strRecord:
  33                 yield '\n'.join(strRecord)
  34                 strRecord = list()
  35             strRecord.append(line.strip())
  36         else:
  37             yield '\n'.join(strRecord)
  38 
  39     def nextRecord(self):
  40         return self.g.next()
  41     def next(self):
  42         lines = self.nextRecord().splitlines()
  43         tcid = lines[0][1:]
  44         tc = TcGo(tcid)
  45         for line in lines[1:]:
  46             tc.addGo(Go(line))
  47         return tc
  48     def __iter__(self):
  49         return self
  50 
  51 class GoTest(unittest.TestCase):
  52     def setUp(self):
  53         self.go = Go('GO:0003774      motor activity          F       GOA_SPTR|P42025~98.57~74')
  54 
  55     def testGo(self):
  56         self.assertEquals('0003774',self.go.id)
  57         self.assertEquals('motor activity',self.go.description)
  58         self.assertEquals('F',self.go.category)
  59 
  60     def testTcGo(self):
  61         tg = TcGo('TC271527')
  62         tg.addGo(self.go)
  63         self.assertEquals('0003774',tg.getGo('0003774').id)
  64 
  65 class GeneratorTest(unittest.TestCase):
  66     def setUp(self):
  67         input = """\
  68 >TC271527
  69 GO:0003774      motor activity          F       GOA_SPTR|P42025~98.57~74
  70 GO:0003779      actin binding           F       FB|FBgn0011745~89.57~74
  71 >TC123456
  72 GO:0015629      actin cytoskeleton              C       FB|FBgn0011745~89.57~74
  73 GO:0005200      structural constituent of cytoskeleton          F       FB|FBgn0011745~89.57~74
  74 >TC111111
  75 GO:0015629      actin cytoskeleton              C       FB|FBgn0011745~89.57~74"""
  76         self.it = TcGoGenerator(StringIO(input))
  77 
  78     def testNextRecord(self):
  79         expected = """\
  80 >TC271527
  81 GO:0003774      motor activity          F       GOA_SPTR|P42025~98.57~74
  82 GO:0003779      actin binding           F       FB|FBgn0011745~89.57~74"""
  83         self.assertEquals(expected, self.it.nextRecord())
  84         expected2 = """\
  85 >TC123456
  86 GO:0015629      actin cytoskeleton              C       FB|FBgn0011745~89.57~74
  87 GO:0005200      structural constituent of cytoskeleton          F       FB|FBgn0011745~89.57~74"""
  88         self.assertEquals(expected2, self.it.nextRecord())
  89         expected3 = """\
  90 >TC111111
  91 GO:0015629      actin cytoskeleton              C       FB|FBgn0011745~89.57~74"""
  92         self.assertEquals(expected3, self.it.nextRecord())
  93         self.assertRaises(StopIteration, self.it.nextRecord)
  94 
  95     def testNextTc(self):
  96         self.assertEquals('TC271527', self.it.next().id)
  97         self.assertEquals('0015629', self.it.next().getGo('0015629').id)
  98 
  99 if __name__=='__main__':
 100     from cStringIO import StringIO
 101     unittest.main()