Source Code for Module Bio.UniGene.UniGene

  1   
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  3  # its documentation with or without modifications and for any purpose 
  4  # and without fee is hereby granted, provided that any copyright 
  5  # notices appear in all copies and that both those copyright notices 
  6  # and this permission notice appear in supporting documentation, and 
  7  # that the names of the contributors or copyright holders not be used 
  8  # in advertising or publicity pertaining to distribution of the software 
  9  # without specific prior permission. 
 10  # 
 11  # THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL 
 12  # WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED 
 13  # WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE 
 14  # CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT 
 15  # OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM 
 16  # LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, 
 17  # NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION 
 18  # WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. 
 19   
 20  import warnings 
 21  from Bio import BiopythonDeprecationWarning 
 22   
 23  warnings.warn("The module Bio.UniGene.UniGene is now deprecated, " 
 24                "and will be removed in a future release of Biopython." 
 25                "To parse UniGene flat files, please use the parser in " 
 26                "Bio.UniGene instead", 
 27                BiopythonDeprecationWarning) 
 28   
 29  import string 
 30  import sgmllib 
 31  import UserDict 
 32  import Bio.File 
 33   
 34   
 35 -class UniGeneParser( sgmllib.SGMLParser ): 
 36   
 37 -    def reset( self ): 
 38          sgmllib.SGMLParser.reset( self ) 
 39          self.text = '' 
 40          self.queue = UserDict.UserDict() 
 41          self.open_tag_stack = [] 
 42          self.open_tag = 'open_html' 
 43          self.key_waiting = '' 
 44          self.master_key = '' 
 45          self.context = 'general_info' 
 46   
 47 -    def parse( self, handle ): 
 48          self.reset() 
 49          self.feed( handle ) 
 50          for key in self.queue: 
 51              if( self.queue[ key ] == {} ): 
 52                  if( key[ :15 ] == 'UniGene Cluster' ): 
 53                      self.queue[ 'UniGene Cluster' ] = key[ 16: ] 
 54                  del self.queue[ key ] 
 55          return self.queue 
 56   
 57  # 
 58  # Assumes an empty line between records 
 59  # 
 60 -    def feed( self, handle ): 
 61          if isinstance(handle, Bio.File.UndoHandle): 
 62              uhandle = handle 
 63          else: 
 64              uhandle = Bio.File.UndoHandle(handle) 
 65          text = '' 
 66          while 1: 
 67              line = uhandle.readline() 
 68              line = string.strip( line ) 
 69              if( line == '' ): 
 70                  break 
 71              text = text + ' ' + line 
 72   
 73          sgmllib.SGMLParser.feed( self, text ) 
 74   
 75 -    def handle_data(self, newtext ): 
 76          newtext = string.strip( newtext ) 
 77          self.text = self.text + newtext 
 78   
 79 -    def start_a( self, attrs ): 
 80          if( self.context == 'seq_info' ): 
 81              if( self.open_tag != 'open_b' ): 
 82                  self.text = '' 
 83   
 84  #        self.queue.append( attrs ) 
 85   
 86 -    def end_a( self ): 
 87          if( self.context == 'seq_info' ): 
 88              if( self.open_tag != 'open_b' ): 
 89                  if( self.key_waiting == '' ): 
 90                      self.key_waiting = self.text 
 91                      self.text = '' 
 92   
 93 -    def start_b( self, attrs ): 
 94   
 95          self.open_tag_stack.append( self.open_tag ) 
 96          self.open_tag = 'open_b' 
 97          if( self.key_waiting == '' ): 
 98              self.text = '' 
 99   
100 -    def end_b( self ): 
101          if( self.text[ :15 ] == 'UniGene Cluster' ): 
102              self.queue[ 'UniGene Cluster' ] = self.text[ 16: ] 
103              self.text = '' 
104          elif( self.key_waiting == '' ): 
105              self.extract_key() 
106   
107 -    def extract_key( self ): 
108          text = string.strip( self.text ) 
109          key = string.join( string.split( text ) ) 
110          words = string.split( key ) 
111          key = string.join( words[ :2 ] ) 
112          self.text = '' 
113   
114          try: 
115              self.open_tag = self.open_tag_stack.pop() 
116          except: 
117              self.open_tag = 'open_html' 
118          if( self.open_tag == 'open_table_data' ): 
119              if( self.context == 'general_info' ): 
120                  if( self.key_waiting == '' ): 
121                      self.key_waiting = key 
122                      self.text = '' 
123              elif( self.context == 'seq_info' ): 
124                  if( text == 'Key to Symbols' ): 
125                      self.context = 'legend' 
126                      self.master_key = key 
127          elif( self.context == 'general_info' ): 
128              self.master_key = key 
129              if 'SEQUENCE' in key: 
130                  self.context = 'seq_info' 
131              self.queue[ key ] = UserDict.UserDict() 
132          elif( self.context == 'seq_info' ): 
133              self.queue[ key ] = UserDict.UserDict() 
134              self.master_key = key 
135   
136 -    def start_table( self, attrs ): 
137          self.open_tag_stack.append( self.open_tag ) 
138          self.open_tag = 'open_table' 
139   
140 -    def end_table( self ): 
141          try: 
142              self.open_tag = self.open_tag_stack.pop() 
143          except: 
144              self.open_tag = 'open_html' 
145          self.key_waiting = '' 
146   
147 -    def start_tr( self, attrs ): 
148          self.open_tag_stack.append( self.open_tag ) 
149          self.open_tag = 'open_table_row' 
150          self.text = '' 
151   
152 -    def end_tr( self ): 
153          try: 
154              self.open_tag = self.open_tag_stack.pop() 
155          except: 
156              self.open_tag = 'open_html' 
157          text = self.text 
158          if text: 
159              self.text = '' 
160              if( text[ 0 ] == ':' ): 
161                  text = text[ 1: ] 
162              text = string.join( string.split( text ) ) 
163              if self.context == 'general_info' or \ 
164                 self.context == 'seq_info': 
165                  try: 
166                      contents = self.queue[ self.master_key ][ self.key_waiting ] 
167                      if isinstance(contents, list): 
168                          contents.append( text ) 
169                      else: 
170                          self.queue[ self.master_key ][ self.key_waiting ] = \ 
171                              [ contents , text ] 
172                  except: 
173                      self.queue[ self.master_key ][ self.key_waiting ] = text 
174   
175                  self.key_waiting = '' 
176   
177 -    def start_td( self, attrs ): 
178          self.open_tag_stack.append( self.open_tag ) 
179          self.open_tag = 'open_table_data' 
180   
181 -    def end_td( self ): 
182          try: 
183              self.open_tag = self.open_tag_stack.pop() 
184          except: 
185              self.open_tag = 'open_html' 
186          if( self.context == 'seq_info' ): 
187              self.text = self.text + ' ' 
188   
189 -    def print_item( self, item, level = 1 ): 
190          indent = '    ' 
191          for j in range( 0, level ): 
192              indent = indent + '    ' 
193          if isinstance(item, str): 
194              if( item != '' ): 
195                  print '%s%s' % ( indent, item ) 
196          elif isinstance(item, list): 
197              for subitem in item: 
198                  self.print_item( subitem, level + 1 ) 
199          elif( isinstance( item, UserDict.UserDict ) ): 
200              for subitem in item: 
201                  print '%skey is %s' % ( indent, subitem ) 
202                  self.print_item( item[ subitem ], level + 1 ) 
203          else: 
204              print item 
205   
206 -    def print_tags( self ): 
207          for key in self.queue: 
208              print 'key %s' % key 
209              self.print_item( self.queue[ key ] ) 
210   
211   
212  if( __name__ == '__main__' ): 
213      handle = open( 'Hs13225.htm') 
214      undo_handle = Bio.File.UndoHandle( handle ) 
215      unigene_parser = UniGeneParser() 
216      unigene_parser.parse( handle ) 
217      unigene_parser.print_tags() 
218