CloneSet42


Clone Mass	Clones in CloneSet	Parameter Count	Clone Similarity	Syntax Category [Sequence Length]
42	2	0	1.000	stmt_list[7]

Clone Abstraction

Parameter Bindings

Clone Instance (Click to see clone)	Line Count	Source Line	Source File
1	42	131	Bio/MEME/Parser.py
2	42	221	Bio/Motif/Parsers/MEME.py

Clone Instance
1

Line Count
42

Source Line
131

Source File

Bio/MEME/Parser.py

    """
    Consumer that can receive events from MEME Scanner.
    
    This is the Consumer object that should be passed to the 
    MEME Scanner.
    """ 

    def __init__ (self): 
         self.current_motif = None 
         self.sequence_names = [ ] 
         self.data = MEMERecord( ) 

    def _version (self,line): 
        line = line.strip( ) 
        ls = line.split( ) 
        self.data.version = ls[2] 

    def _datafile (self,line): 
        line = line.strip( ) 
        line = line.replace("DATAFILE= ","") 
        self.data.datafile = line 

    def _alphabet (self,line): 
        line = line.strip( ) 
        line = line.replace("ALPHABET= ","") 
        if line=="ACGT":  
            al = IUPAC.unambiguous_dna 
        else: 
             al = IUPAC.protein 
        self.data.alphabet = al 

    def _sequence_name (self,line): 
        line = line.strip( ) 
        ls = line.split( ) 
        self.data.sequence_names.append(ls[0]) 
        if len(ls)==6:  
            self.data.sequence_names.append(ls[3]) 
        

    def _commandline (self,line): 
        line = line.strip( ) 
        line = line.replace("command: ","") 
        self.data.command = line

Clone Instance
2

Line Count
42

Source Line
221

Source File

Bio/Motif/Parsers/MEME.py

    """
    Consumer that can receive events from MEME Scanner.
    
    This is the Consumer object that should be passed to the 
    MEME Scanner.
    """ 

    def __init__ (self): 
         self.current_motif = None 
         self.sequence_names = [ ] 
         self.data = MEMERecord( ) 

    def _version (self,line): 
        line = line.strip( ) 
        ls = line.split( ) 
        self.data.version = ls[2] 

    def _datafile (self,line): 
        line = line.strip( ) 
        line = line.replace("DATAFILE= ","") 
        self.data.datafile = line 

    def _alphabet (self,line): 
        line = line.strip( ) 
        line = line.replace("ALPHABET= ","") 
        if line=="ACGT":  
            al = IUPAC.unambiguous_dna 
        else: 
             al = IUPAC.protein 
        self.data.alphabet = al 

    def _sequence_name (self,line): 
        line = line.strip( ) 
        ls = line.split( ) 
        self.data.sequence_names.append(ls[0]) 
        if len(ls)==6:  
            self.data.sequence_names.append(ls[3]) 
        

    def _commandline (self,line): 
        line = line.strip( ) 
        line = line.replace("command: ","") 
        self.data.command = line

Clone Abstraction

Parameter Count: 0

Parameter Bindings

"""
    Consumer that can receive events from MEME Scanner.
    
    This is the Consumer object that should be passed to the 
    MEME Scanner.
    """ 

def __init__(self):
  self.current_motif = None 
  self.sequence_names = [ ] 
  self.data = MEMERecord( ) 

def _version(self,line):
  line = line.strip( ) 
  ls = line.split( ) 
  self.data.version = ls[2] 

def _datafile(self,line):
  line = line.strip( ) 
  line = line.replace("DATAFILE= ","") 
  self.data.datafile = line 

def _alphabet(self,line):
  line = line.strip( ) 
  line = line.replace("ALPHABET= ","") 
  if line=="ACGT":
  
    al = IUPAC.unambiguous_dna 
  else:
  
    al = IUPAC.protein 
  self.data.alphabet = al 

def _sequence_name(self,line):
  line = line.strip( ) 
  ls = line.split( ) 
  self.data.sequence_names.append(ls[0]) 
  if len(ls)==6:
  
    self.data.sequence_names.append(ls[3]) 
  

def _commandline(self,line):
  line = line.strip( ) 
  line = line.replace("command: ","") 
  self.data.command = line

CloneAbstraction

Parameter Bindings
Parameter Index	Clone Instance	Parameter Name	Value
None