CloneSet131


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
21201.000file_input_element_list[4]
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
120218
Bio/SeqUtils/__init__.py
22124
Scripts/xbbtools/nextorf.py
Clone Instance
1
Line Count
20
Source Line
218
Source File
Bio/SeqUtils/__init__.py

class ProteinX(Alphabet.ProteinAlphabet): 
     letters = IUPACData.extended_protein_letters+"X" 

proteinX = ProteinX( ) 

class MissingTable: 

     def __init__(self,table): 
         self._table = table 

     def get(self,codon,stop_symbol):  
         try :
             
             return self._table.get(codon,stop_symbol) 
         except CodonTable.TranslationError: 
              return "X" 
         

def makeTableX(table): 
     assert table.protein_alphabet==IUPAC.extended_protein 
     return CodonTable.CodonTable(table.nucleotide_alphabet,proteinX,MissingTable(table.forward_table),table.back_table,table.start_codons,table.stop_codons) 




 # end of hacks


Clone Instance
2
Line Count
21
Source Line
24
Source File
Scripts/xbbtools/nextorf.py

class ProteinX(Alphabet.ProteinAlphabet): 
    letters = IUPACData.extended_protein_letters+"X" 

proteinX = ProteinX( ) 

class MissingTable: 

   def __init__(self,table): 
     self._table = table 

   def get(self,codon,stop_symbol):  
     try :
         
       return self._table.get(codon,stop_symbol) 
     except CodonTable.TranslationError: 
        return "X" 

  # Make the codon table given an existing table
     

def makeTableX(table): 
   assert table.protein_alphabet==IUPAC.extended_protein 
   return CodonTable.CodonTable(table.nucleotide_alphabet,proteinX,MissingTable(table.forward_table),table.back_table,table.start_codons,table.stop_codons) 


Clone AbstractionParameter Count: 0Parameter Bindings

class ProteinX(Alphabet.ProteinAlphabet):
  letters = IUPACData.extended_protein_letters+"X" 
proteinX = ProteinX( ) 

class MissingTable:

  def __init__(self,table):
  
    self._table = table 

  def get(self,codon,stop_symbol):
  
    try :
    
      return self._table.get(codon,stop_symbol) 
    except CodonTable.TranslationError:
    
      return "X" 
      # Make the codon table given an existing table
    

def makeTableX(table):
  assert table.protein_alphabet==IUPAC.extended_protein 
  return CodonTable.CodonTable(table.nucleotide_alphabet,proteinX,MissingTable(table.forward_table),table.back_table,table.start_codons,table.stop_codons) 
  # end of hacks
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
None