Source Code for Module Bio.AlignAce.Parser

  1  # Copyright 2003 by Bartek Wilczynski.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5  """ 
  6  Classes for parsing AlignAce and CompareACE files. 
  7   
  8  This module is DEPRECATED; please use Bio.Motif.Parsers.AlignAce instead. 
  9  """ 
 10   
 11  import warnings 
 12  warnings.warn('Bio.AlignAce is deprecated. Please use Bio.Motif instead.', 
 13                DeprecationWarning) 
 14   
 15   
 16  from Bio.ParserSupport import * 
 17  from Scanner import AlignAceScanner,CompareAceScanner 
 18  from Motif import Motif 
 19  from Bio.Alphabet import IUPAC 
 20  from Bio.Seq import Seq 
 21   
 22   
 23 -class AlignAceConsumer: 
 24      """ 
 25      The general purpose consumer for the AlignAceScanner. 
 26   
 27      Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property. 
 28      """ 
 29 -    def __init__(self): 
 30          self.motifs=[] 
 31          self.current_motif=None 
 32          self.param_dict = None 
 33       
 34 -    def parameters(self,line): 
 35          self.param_dict={} 
 36   
 37 -    def parameter(self,line): 
 38          par_name = line.split("=")[0].strip() 
 39          par_value = line.split("=")[1].strip() 
 40          self.param_dict[par_name]=par_value 
 41           
 42 -    def sequences(self,line): 
 43          self.seq_dict=[] 
 44           
 45 -    def sequence(self,line): 
 46          seq_name = line.split("\t")[1] 
 47          self.seq_dict.append(seq_name) 
 48           
 49 -    def motif(self,line): 
 50          self.current_motif = Motif() 
 51          self.motifs.append(self.current_motif) 
 52          self.current_motif.alphabet=IUPAC.unambiguous_dna 
 53           
 54 -    def motif_hit(self,line): 
 55          seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna) 
 56          self.current_motif.add_instance(seq) 
 57           
 58 -    def motif_score(self,line): 
 59          self.current_motif.score = float(line.split()[-1]) 
 60           
 61 -    def motif_mask(self,line): 
 62          self.current_motif.set_mask(line.strip("\n\c")) 
 63   
 64 -    def noevent(self,line): 
 65          pass 
 66           
 67 -    def version(self,line): 
 68          self.ver = line 
 69           
 70 -    def command_line(self,line): 
 71          self.cmd_line = line 
 72       
 73 -class AlignAceParser(AbstractParser): 
 74      """Parses AlignAce data into a sequence of Motifs. 
 75      """ 
 76 -    def __init__(self): 
 77          """__init__(self)""" 
 78          self._scanner = AlignAceScanner() 
 79          self._consumer = AlignAceConsumer() 
 80   
 81 -    def parse(self, handle): 
 82          """parse(self, handle)""" 
 83          self._scanner.feed(handle, self._consumer) 
 84          return self._consumer.motifs 
 85   
 86   
 87 -class CompareAceConsumer: 
 88      """ 
 89      The general purpose consumer for the CompareAceScanner. 
 90   
 91      Should be passed as the consumer to the feed method of the CompareAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property. 
 92      """ 
 93 -    def __init__(self): 
 94          pass 
 95 -    def motif_score(self,line): 
 96          self.data = float(line.split()[-1]) 
 97       
 98 -class CompareAceParser(AbstractParser): 
 99      """Parses CompareAce output to usable form 
100   
101      ### so far only in a very limited way 
102      """ 
103 -    def __init__(self): 
104          """__init__(self)""" 
105          self._scanner = CompareAceScanner() 
106          self._consumer = CompareAceConsumer() 
107   
108 -    def parse(self, handle): 
109          """parse(self, handle)""" 
110          self._scanner.feed(handle, self._consumer) 
111          return self._consumer.data 
112