programmation Python aide

Question

J'ai ce fichier python que je travaille sur:

class Range: 
    """ An object that has a non-negative start position and a non-negative length""" 
    def __init__(self, start, end): 
       """ 
       Function: generates a new Range 
       Returns : a new range 
       Args : start - start position 
          end - end position 
       Start and End must be non-negative """ 
       self.start = 0 
       self.end = 10000 
     self.setStart(start) 
     self.setEnd(end) 
    def getStart(self): 
       """ 
       Function: get the start of the range 
       Returns : a number or None 
       Args : start - the int index of the first nucleotide of this range """ 
     return self.start 
    def setStart(self, s): 
       """ 
       Function: set the start of the range 
       Returns : None 
       Args : start - a non-negative int or None """ 
       if type(s) !=int: 
         raise TypeError ("Cannot set Start as this is not an interger") 
       elif s < 0: 
         raise ValueError ("Cannot set Start as this is not a non-negative int") 
       elif s > self.end: 
         raise ValueError("start cannot be larger than end") 
       else: 
         self.start = s 
    def getEnd(self): 
       """ 
       Function: get the end of the range 
       Returns : a number 
       Args : 
       """ 
     return self.end 
    def setEnd(self, e): 
       """ 
       Function: set the end of the range 
       Returns : None 
       Args : end - a non-negative int or None 
       """ 
       if type(e) !=int: 
         raise TypeError ("Cannot set End as this is not an interger") 
       elif e < 0: 
         raise ValueError ("Cannot set End as this is not a non-negative int") 
       elif e < self.start: 
         raise ValueError ("end has to be larger than start") 
       else: 
         self.end = e 
    def getLength(self): 
       """ 
       Function: get the length of the range 
       Returns : an int. the length of this range 
       Args: 
       """ 
       return self.end - self.start 
    def overlaps(self, r): 
       """ 
       Function: to test if two nucleotide is overlap 
       Returns : True or False 
       Args : other - a Range object 
       """ 
       start1 = self.getStart() 
       end1 = start1 + self.getLength() 
       start2 = r.getStart() 
       end2 = start2 + self.getLength() 
       max_start = max(start1,start2) 
       min_end = min(end1,end2) 
       return min_end - max_start > 0 
     if self.getStart() == r.getStart(): 
         return True 
     else: 
      return False 

class DNAFeature(Range): 
     """Represents a feature on a DNA sequence """ 
     def __init__(self, seq_name = None, strand = 0, **kwargs): 
       """ 
       Function : represents a rane 
       Returns : 
       Args  : strand, seqname, **kwargs 
       """   
       Range.__init__(self, **kwargs) 
       self.setStrand(strand) 
       self.setSeqName(seq_name) 
     def getSeqName(self): 
       """ 
       Function: Gets object's Sequence Name 
       Returns : seqname - string 
       Args : 
       """ 
       return self.seq_name 
     def setSeqName(self, seq_name): 
       """ 
       Function: Sets object's Sequence Name 
       Returns : None 
       Args : seqname - mRNA accession name 
       """ 
     self.seq_name = seq_name 
     def getStrand(self): 
       """ 
       Function: Retrieve the strand affiliation of this 
       Returns : 1, 0, -1 - strand 
       Args : 
       """ 
       return self.strand 
     def setStrand(self, strand): 
       """ 
       Function: sets which strand the object is on 
       Returns : None 
       Args : strand - one of ['+',1,'F','-',-1,'R'] 
       """ 
       StrandValues = [1, 0, -1] 

     if not strand in StrandValues: 
      raise ValueError("only able to setStrand if the values is 1, 0, or -1") 
     else: 
         self.strand = strand 
     def overlaps(self, other, ignore_strand = True): 
       """ 
       Function: tests if this overlaps other 
       Returns : true if the ranges have same Seqname and overlap, false if not 
       Args : other - another Range object 
       """ 
       if ignore_strand == True and self.getSeqName() == other.getSeqName(): 
        return Range.overlaps(self,other) 
       else: 
        return False 

class GeneModel(DNAFeature): 
     def __init__(self, transl_start=None, transl_stop=None, display_id = None, **kwargs): 
       """ 
       Function : contains a group of DNAFeature objects representing exons 
       Returns : 
       Args  : **kwargs 
       """ 
       DNAFeature.__init__(self, **kwargs) 
       self.setTranslStart(transl_start) 
       self.setTranslStop(transl_stop) 
       self.setDisplayId(display_id) 
       self.exons = [ ] 
     def getFeats(self): 
       """ 
       Function: gets object's feats list 
       Returns : list of feature keys 
       Args : feature_type - the type of strand the object holds 
       """ 
       self.exons.sort(cmp=self.start) 
       return self.exons 
     def addFeat(self, feat): 
       """ 
       Function: adds SeqFeature to feats keys 
       Returns : None 
       Args : feat - a single SeqFeature object 
       """ 
       if type(feat) == DNAFeature: 
         self.exons.append(feat) 
       else: 
         raise TypeError("Cannot add feature as it is not a type of DNAFeature") 
     def setTranslStart(self, transl_start): 
       """ 
       Function : accepts an non-negative int, sets the start position of the initiating ATG 
       Returns : 
       Args  : transl_start 
       """ 
       if transl_start == None: 
        self.transl_start = None 
        return 
       elif type(transl_start) !=int: 
        raise TypeError("TranslStart cannot be set since it is not a type of int") 
       elif transl_start < 0: 
        raise ValueError("TranslStart cannot be set to a negative int") 
       else: 
        self.translStart = transl_start 
     def getTranslStart(self): 
       """ 
       Function: the start position of initiating ATG codon 
       Return : an int. 
       Args : 
       """ 
       return self.transl_start 
     def setTranslStop(self, transl_stop): 
       """ 
       Function: set the end position of initiating ATG codon 
       Return : None 
       Args : a positive int 
       """ 
       if transl_stop == None: 
        self.transl_stop = None 
        return 
       elif type(transl_stop) !=int: 
        raise TypeError("TranslStop cannot be set since it is not a type of int") 
       elif transl_stop < 0: 
        raise ValueError("TranslStop cannot be set to a negative int") 
       else: 
        self.translStop = transl_stop 
     def getTranslStop(self): 
       """ 
       Function: the end position of initiating ATG codon 
       Return : an int. 
       Args : 
       """ 
       return self.transl_stop 
     def setDisplayId(self, display_id): 
       """ 
       Function: set the display id 
       Returns : None 
       Args : display_id - a string, a preferred name for this 
       """ 
       if type(display_id) !=str: 
         raise TypeError("Cannot set displayId as it is not a type string") 
       else: 
         self.display_id = display_id 
     def getDisplayId(self): 
       """ 
       Function: get the display id 
       Returns : display_id - a string, a preferred name for this, e.g AT1G10555.1 
       Args : 
       """ 
       return self.display_id 

Ensuite, je suis arrivé un code de mon professeur pour tester mon dossier:

class TestGeneModelConstructor(unittest.TestCase): 
    def testGeneModelConstructor(self): 
     """GeneModel constructor supports named arguments display_id,transl_start,transl_stop""" 
     p1.GeneModel(start=0,end=10,seq_name='something',strand=1,display_id='foobar', 
        transl_start=0,transl_stop=10) 

    def testGeneModelConstructorDefaults(self): 
     """Default values for display_id, transl_start, transl_stop should be None""" 
     r = p1.GeneModel() 
     self.assertEquals(r.getDisplayId(),None) 
     self.assertEquals(r.getTranslStart(),None) 
     self.assertEquals(r.getTranslStop(),None) 

    def testGeneModelConstructorWrongTypeDisplayId(self): 
     """Raise a TypeError if display_id is not a string.""" 
     self.assertRaises(TypeError,p1.GeneModel,display_id=0) 

    def testGeneModelConstructorWrongTypeTranslStart(self): 
     """Raise a TypeError if transl_start is not an int.""" 
     self.assertRaises(TypeError,p1.GeneModel,transl_start='0') 

    def testGeneModelConstructorWrongTypeTranslStop(self): 
     """Raise a TypeError if transl_stop is not an int.""" 
     self.assertRaises(TypeError,p1.GeneModel,transl_stop='0') 

    def testGeneModelConstructorWrongValueTranslStart(self): 
     """Raise a ValueError if transl_start is int < 0.""" 
     self.assertRaises(ValueError,p1.GeneModel,transl_start=-1) 

    def testGeneModelConstructorWrongValueTranslStop(self): 
     """Raise a ValueError if transl_stop is int < 0.""" 
     self.assertRaises(ValueError,p1.GeneModel,transl_stop=-1) 

Je l'exécuter et a obtenu ces erreurs:

ERROR: Default values for display_id, transl_start, transl_stop should be None 
---------------------------------------------------------------------- 
Traceback (most recent call last): 
    File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 117, in testGeneModelConstructorDefaults 
    r = p1.GeneModel() 
TypeError: __init__() takes at least 3 arguments (1 given) 

====================================================================== 
ERROR: Raise a ValueError if transl_start is int < 0. 
---------------------------------------------------------------------- 
Traceback (most recent call last): 
    File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 136, in testGeneModelConstructorWrongValueTranslStart 
    self.assertRaises(ValueError,p1.GeneModel,transl_start=-1) 
    File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/unittest.py", line 336, in failUnlessRaises 
TypeError: __init__() takes at least 3 non-keyword arguments (2 given) 

====================================================================== 
ERROR: Raise a ValueError if transl_stop is int < 0. 
---------------------------------------------------------------------- 
Traceback (most recent call last): 
    File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 140, in testGeneModelConstructorWrongValueTranslStop 
    self.assertRaises(ValueError,p1.GeneModel,transl_stop=-1) 
    File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/unittest.py", line 336, in failUnlessRaises 
TypeError: __init__() takes at least 3 non-keyword arguments (1 given) 

Je ne sais pas ce qui est faux, je l'ai essayé de fixes, il ou deux fois, mais ne l'ai pas comprendre ce qui est mal dans mes codes.

Bon, je dois changer mon code dans DNAFeature comme ceci:

class DNAFeature(Range): 
    """Represents a feature on a DNA sequence """ 
    def __init__(self, seq_name = None, strand = 0, **kwargs): 
      """ 
      Function : represents a rane 
      Returns : 
      Args  : strand, seqname, **kwargs 
      """   
      Range.__init__(self, 0,10000, **kwargs) 
      self.setStrand(strand) 
      self.setSeqName(seq_name) 

Et puis, obtenir plus de 3 erreurs et 1 échec comme celui-ci:

ERROR: DNAFeature on different sequence don't overlap 
---------------------------------------------------------------------- 
    Traceback (most recent call last): 
    File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 164, in testDiffSequenceOverlaps 
    r1 = p1.DNAFeature(start=0,end=10,strand=1,seq_name="foo") 
    File "/Users/trungpham/binf_prog/tpham22/project1/p1.py", line 95, in __init__ 
    Range.__init__(self, 0, 10000, **kwargs) 
TypeError: __init__() got multiple values for keyword argument 'start' 

====================================================================== 
ERROR: DNAFeatures on the same strand can overlap if ignore_strand is True. 
---------------------------------------------------------------------- 
    Traceback (most recent call last): 
    File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 185, in testDiffStrandsDontOverlap 
    r1 = p1.DNAFeature(start=0,end=10,strand=1,seq_name="foo") 
    File "/Users/trungpham/binf_prog/tpham22/project1/p1.py", line 95, in __init__ 
    Range.__init__(self, 0, 10000, **kwargs) 
TypeError: __init__() got multiple values for keyword argument 'start' 

====================================================================== 
ERROR: GeneModel constructor supports named arguments display_id,transl_start,transl_stop 
---------------------------------------------------------------------- 
    Traceback (most recent call last): 
     File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 113, in testGeneModelConstructor 
    transl_start=0,transl_stop=10) 
    File "/Users/trungpham/binf_prog/tpham22/project1/p1.py", line 151, in __init__ 
    DNAFeature.__init__(self, **kwargs) 
     File "/Users/trungpham/binf_prog/tpham22/project1/p1.py", line 95, in __init__ 
    Range.__init__(self, 0, 10000, **kwargs) 
TypeError: __init__() got multiple values for keyword argument 'start' 

FAIL: Raise a TypeError if seq_name is not a string. 
---------------------------------------------------------------------- 
Traceback (most recent call last): 
    File "/Users/trungpham/binf_prog/class/test/testProject1.py", line 98, in testDNAFeatureSeqNameConstructorWrongType 
    self.assertRaises(TypeError,p1.DNAFeature,seq_name=0) 
AssertionError: TypeError not raised 

Answer 1

Il y a plusieurs choses mauvaises:

Premièrement:

Dans votre fonction de test, testGeneModelConstructorDefaults, vous avez le commentaire suivant: "Les valeurs par défaut pour display_id, transl_start, transl_stop doit être None". Le problème que vous voyez est que vous avez seulement mis en place les valeurs par défaut sur 1 des 3 arguments; Cette fonction de test suppose que vous avez défini les paramètres par défaut sur les trois. Pour résoudre ce problème, vous devez définir le constructeur comme ceci:

def __init__(self, transl_start=None, transl_stop=None, display_id = None, **kwargs) 

En ayant les arguments de mots clés, il utilisera la valeur par défaut de None. Si vous ne spécifiez pas explicitement ces arguments, Python se plaindra (comme il le fait actuellement).

En second lieu:

Vous devez considérer vos constructeurs de superclasse. La superclasse Range demande deux paramètres: début et fin.

def __init__(self, start, end): 

Cependant, lorsque le constructeur DNAFeature appelle les Range superclasse, il ne passe pas commencer ou se terminer:

Range.__init__(self, **kwargs) 

Ce est là que je pense que l'erreur est maintenant (je pense avant c'était à l'appel p1.GeneModel() - il y a probablement différentes lignes d'erreur dans vos deux messages d'erreur).

Pour résoudre ce problème, définissez également les valeurs de début et de fin dans les paramètres de mot-clé.Ainsi, au lieu de:

def __init__(self, start, end): 

faire:

def __init__(self, start=0, end=10000): 

Vous pouvez ensuite supprimer les lignes de code ci-dessous dans votre constructeur range:

self.start = 0 
self.end = 10000 

Cela devrait au moins obtenir vous passé ce erreur - vous pouvez trouver plus d'erreurs que vous avez.

Answer 2

Il semble que les tests assument que tous les paramètres sont passés par valeur. Vous devez donner les arguments positionnels par défaut.

Answer 3

Smashery est juste. Essayez d'exécuter ce code simplifié:

class GeneModel(object): 
    def __init__(self, transl_start=None, transl_stop=None, display_id = None, **kwargs): 
     pass 

def testGeneModelConstructor(): 
    g = GeneModel(start=0,end=10,seq_name='something',strand=1,display_id='foobar', transl_start=0,transl_stop=10) 

def testGeneModelConstructorDefaults(): 
    r = GeneModel() 

testGeneModelConstructor() 
testGeneModelConstructorDefaults()