CloneSet35


Previous CloneSetNext CloneSetBack to Main Report
Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
74201.000file_input_element_list[2]
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
1749
Bio/AlignAce/Scanner.py
27479
Bio/Motif/Parsers/AlignAce.py
Clone Instance
1
Line Count
74
Source Line
9
Source File
Bio/AlignAce/Scanner.py

class AlignAceScanner: 
     """Scannner for AlignACE output

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    noevent - blank line

    version - AlignACE version number
    command_line - AlignACE command line string
    parameters - the begining of the parameters
    parameter - the line containing a parameter
    sequences - the begining of the sequences list
    sequence - line containing the name of the input sequence (and a respective number)
    motif - the begining of the motif (contains the number)
    motif_hit - one hit for a motif
    motif_mask - mask of the motif (space - gap, asterisk - significant position)
    motif_score - MAP score of the motif - approx. N * log R, where R == (num. of actual occur.) / (num. of occur. expected by random.)
    
    """ 

     def feed(self,handle,consumer):  
         """S.feed(handle, consumer)

        Feed in a AlignACE report for scanning.  handle is a file-like
        object that contains the AlignACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """ 
         consumer.version(handle.readline( )) 
         consumer.command_line(handle.readline( )) 
         for line in handle: 
              if line.strip( )=="": 
                  consumer.noevent(line) 
              elif line[ :4]=="Para":
                                    
                  consumer.parameters(line) 
              elif line[0]=="#": 
                   consumer.sequence(line) 
              elif "=" in line: 
                   consumer.parameter(line) 
              elif line[ :5]=="Input":
                                     
                  consumer.sequences(line) 
              elif line[ :5]=="Motif":
                                     
                  consumer.motif(line) 
              elif line[ :3]=="MAP":
                                   
                  consumer.motif_score(line) 
              elif len(line.split("\t"))==4: 
                   consumer.motif_hit(line) 
              elif "*" in line: 
                   consumer.motif_mask(line) 
              else: 
                   raise ValueError(line) 
              

class CompareAceScanner: 
     """Scannner for CompareACE output

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    motif_score - CompareACE score of motifs

    ###### TO DO #############3
    extend the scanner to include other, more complex outputs.
    """ 

     def feed(self,handle,consumer):  
         """S.feed(handle, consumer)

        Feed in a CompareACE report for scanning.  handle is a file-like
        object that contains the CompareACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """ 
         consumer.motif_score(handle.readline( )) 
     


Clone Instance
2
Line Count
74
Source Line
79
Source File
Bio/Motif/Parsers/AlignAce.py

class AlignAceScanner: 
     """Scannner for AlignACE output

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    noevent - blank line

    version - AlignACE version number
    command_line - AlignACE command line string
    parameters - the begining of the parameters
    parameter - the line containing a parameter
    sequences - the begining of the sequences list
    sequence - line containing the name of the input sequence (and a respective number)
    motif - the begining of the motif (contains the number)
    motif_hit - one hit for a motif
    motif_mask - mask of the motif (space - gap, asterisk - significant position)
    motif_score - MAP score of the motif - approx. N * log R, where R == (num. of actual occur.) / (num. of occur. expected by random.)
    
    """ 

     def feed(self,handle,consumer):  
         """S.feed(handle, consumer)

        Feed in a AlignACE report for scanning.  handle is a file-like
        object that contains the AlignACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """ 
         consumer.version(handle.readline( )) 
         consumer.command_line(handle.readline( )) 
         for line in handle: 
              if line.strip( )=="": 
                  consumer.noevent(line) 
              elif line[ :4]=="Para":
                                    
                  consumer.parameters(line) 
              elif line[0]=="#": 
                   consumer.sequence(line) 
              elif "=" in line: 
                   consumer.parameter(line) 
              elif line[ :5]=="Input":
                                     
                  consumer.sequences(line) 
              elif line[ :5]=="Motif":
                                     
                  consumer.motif(line) 
              elif line[ :3]=="MAP":
                                   
                  consumer.motif_score(line) 
              elif len(line.split("\t"))==4: 
                   consumer.motif_hit(line) 
              elif "*" in line: 
                   consumer.motif_mask(line) 
              else: 
                   raise ValueError(line) 
              

class CompareAceScanner: 
     """Scannner for CompareACE output

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    motif_score - CompareACE score of motifs

    ###### TO DO #############3
    extend the scanner to include other, more complex outputs.
    """ 

     def feed(self,handle,consumer):  
         """S.feed(handle, consumer)

        Feed in a CompareACE report for scanning.  handle is a file-like
        object that contains the CompareACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """ 
         consumer.motif_score(handle.readline( )) 
     


Clone AbstractionParameter Count: 0Parameter Bindings

class AlignAceScanner:
  """Scannner for AlignACE output

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    noevent - blank line

    version - AlignACE version number
    command_line - AlignACE command line string
    parameters - the begining of the parameters
    parameter - the line containing a parameter
    sequences - the begining of the sequences list
    sequence - line containing the name of the input sequence (and a respective number)
    motif - the begining of the motif (contains the number)
    motif_hit - one hit for a motif
    motif_mask - mask of the motif (space - gap, asterisk - significant position)
    motif_score - MAP score of the motif - approx. N * log R, where R == (num. of actual occur.) / (num. of occur. expected by random.)
    
    """ 

  def feed(self,handle,consumer):
  
    """S.feed(handle, consumer)

        Feed in a AlignACE report for scanning.  handle is a file-like
        object that contains the AlignACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """ 
    consumer.version(handle.readline( )) 
    consumer.command_line(handle.readline( )) 
    for line in handle:
    
      if line.strip( )=="":
      
        consumer.noevent(line) 
      elif line[ :4]=="Para":
      
        consumer.parameters(line) 
      elif line[0]=="#":
      
        consumer.sequence(line) 
      elif "=" in line:
      
        consumer.parameter(line) 
      elif line[ :5]=="Input":
      
        consumer.sequences(line) 
      elif line[ :5]=="Motif":
      
        consumer.motif(line) 
      elif line[ :3]=="MAP":
      
        consumer.motif_score(line) 
      elif len(line.split("\t"))==4:
      
        consumer.motif_hit(line) 
      elif "*" in line:
      
        consumer.motif_mask(line) 
      else:
      
        raise ValueError(line) 
      

class CompareAceScanner:
  """Scannner for CompareACE output

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    motif_score - CompareACE score of motifs

    ###### TO DO #############3
    extend the scanner to include other, more complex outputs.
    """ 

  def feed(self,handle,consumer):
  
    """S.feed(handle, consumer)

        Feed in a CompareACE report for scanning.  handle is a file-like
        object that contains the CompareACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """ 
    consumer.motif_score(handle.readline( )) 
  
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
None