CloneSet36

Bio/ExPASy/Prosite.py

Bio/Prosite/__init__.py

            #Expect CC lines like this:
            #CC   /TAXO-RANGE=??EPV; /MAX-REPEAT=2;
            #Can (normally) split on ";" and then on "="
            cols = value.split(";") 
            for col in cols: 
                 if not col or col[ :17]=="Automatic scaling": 
                     # DNAJ_2 in Release 15 has a non-standard comment line:
                     # CC   Automatic scaling using reversed database
                     # Throw it away.  (Should I keep it?)
                     continue 
                 if col.count("=")==0:   
                     #Missing qualifier!  Can we recover gracefully?
                     #For example, from Bug 2403, in PS50293 have:
                     #CC /AUTHOR=K_Hofmann; N_Hulo
                     continue 
                 qual,data =  [word.lstrip( ) for word in col.split("=")] 
                 if qual=="/TAXO-RANGE":  
                     record.cc_taxo_range = data 
                 elif qual=="/MAX-REPEAT":  
                     record.cc_max_repeat = data 
                 elif qual=="/SITE":  
                     pos,desc =  data.split(",") 
                     record.cc_site.append((int(pos),desc)) 
                 elif qual=="/SKIP-FLAG":  
                     record.cc_skip_flag = data 
                 elif qual=="/MATRIX_TYPE":  
                     record.cc_matrix_type = data 
                 elif qual=="/SCALING_DB":  
                     record.cc_scaling_db = data 
                 elif qual=="/AUTHOR":  
                     record.cc_author = data 
                 elif qual=="/FT_KEY":  
                     record.cc_ft_key = data 
                 elif qual=="/FT_DESC":  
                     record.cc_ft_desc = data 
                 elif qual=="/VERSION":  
                     record.cc_version = data 
                 else: 
                      raise ValueError("""Unknown qual %s in comment line
%s"""                                  %(repr(qual),line)) 
                 

        #Expect CC lines like this:
        #CC   /TAXO-RANGE=??EPV; /MAX-REPEAT=2;
        #Can (normally) split on ";" and then on "="
        cols = self._clean(line).split(";") 
        for col in cols: 
             if not col or col[ :17]=="Automatic scaling": 
                 # DNAJ_2 in Release 15 has a non-standard comment line:
                 # CC   Automatic scaling using reversed database
                 # Throw it away.  (Should I keep it?)
                 continue 
             if col.count("=")==0:   
                 #Missing qualifier!  Can we recover gracefully?
                 #For example, from Bug 2403, in PS50293 have:
                 #CC /AUTHOR=K_Hofmann; N_Hulo
                 continue 
             qual,data =  [word.lstrip( ) for word in col.split("=")] 
             if qual=="/TAXO-RANGE":  
                 self.data.cc_taxo_range = data 
             elif qual=="/MAX-REPEAT":  
                 self.data.cc_max_repeat = data 
             elif qual=="/SITE":  
                 pos,desc =  data.split(",") 
                 self.data.cc_site.append((int(pos),desc)) 
             elif qual=="/SKIP-FLAG":  
                 self.data.cc_skip_flag = data 
             elif qual=="/MATRIX_TYPE":  
                 self.data.cc_matrix_type = data 
             elif qual=="/SCALING_DB":  
                 self.data.cc_scaling_db = data 
             elif qual=="/AUTHOR":  
                 self.data.cc_author = data 
             elif qual=="/FT_KEY":  
                 self.data.cc_ft_key = data 
             elif qual=="/FT_DESC":  
                 self.data.cc_ft_desc = data 
             elif qual=="/VERSION":  
                 self.data.cc_version = data 
             else: 
                  raise ValueError("""Unknown qual %s in comment line
%s"""                              %(repr(qual),line)) 
             

  #Expect CC lines like this:
  #CC   /TAXO-RANGE=??EPV; /MAX-REPEAT=2;
  #Can (normally) split on ";" and then on "="
  cols = [[#variable5ecc2480]].split(";") 
  for col in cols:
  
    if not col or col[ :17]=="Automatic scaling":
    
      # DNAJ_2 in Release 15 has a non-standard comment line:
      # CC   Automatic scaling using reversed database
      # Throw it away.  (Should I keep it?)
      continue 
    if col.count("=")==0:
    
      #Missing qualifier!  Can we recover gracefully?
      #For example, from Bug 2403, in PS50293 have:
      #CC /AUTHOR=K_Hofmann; N_Hulo
      continue 
    qual,data = [word.lstrip( ) for word in col.split("=")] 
    if qual=="/TAXO-RANGE":
    
       [[#variable72f275a0]].cc_taxo_range = data 
    elif qual=="/MAX-REPEAT":
    
       [[#variable72f275a0]].cc_max_repeat = data 
    elif qual=="/SITE":
    
      pos,desc = data.split(",") 
       [[#variable5ecc2420]].cc_site.append((int(pos),desc)) 
    elif qual=="/SKIP-FLAG":
    
       [[#variable72f275a0]].cc_skip_flag = data 
    elif qual=="/MATRIX_TYPE":
    
       [[#variable72f275a0]].cc_matrix_type = data 
    elif qual=="/SCALING_DB":
    
       [[#variable72f275a0]].cc_scaling_db = data 
    elif qual=="/AUTHOR":
    
       [[#variable72f275a0]].cc_author = data 
    elif qual=="/FT_KEY":
    
       [[#variable72f275a0]].cc_ft_key = data 
    elif qual=="/FT_DESC":
    
       [[#variable72f275a0]].cc_ft_desc = data 
    elif qual=="/VERSION":
    
       [[#variable72f275a0]].cc_version = data 
    else:
    
      raise ValueError("""Unknown qual %s in comment line
%s"""                  %(repr(qual),line)) 
    
 

value 

self._clean(line) 

record 

self.data 

record 

self.data