# Copyright 2000 by Katharine Lindner. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Rebase.py This module provides code to work with files from http://rebase.neb.com/rebase/rebase.html Classes: Record Holds rebase sequence data. Iterator Iterates over sequence data in a rebase file. Dictionary Accesses a rebase file using a dictionary interface. RecordParser Parses rebase sequence data into a Record object. _Scanner Scans a rebase-format stream. _RecordConsumer Consumes rebase data to a Record object. Functions: index_file Index a FASTA file for a Dictionary. """ from types import * import string from Bio import File from Bio import Index import urllib import sgmllib from Bio.ParserSupport import * import Bio.File import UserDict class Record: """Holds information from a Rebase record. Members: seq_5_to_3 The sequence. seq_3_to_5 """ def __init__(self ): """__init__(self ) Create a new Record. """ self.seq_5_to_3 = '' self.seq_3_to_5 = '' class Iterator: """Returns one record at a time from a Rebase file. Methods: next Return the next record from the stream, or None. """ def __init__(self, handle, parser=None): """__init__(self, handle, parser=None) Create a new iterator. handle is a file-like object. parser is an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. """ if type(handle) is not FileType and type(handle) is not InstanceType: raise ValueError, "I expected a file handle or file-like object" self._uhandle = SGMLHandle( File.UndoHandle( handle ) ) self._parser = parser def next(self): """next(self) -> object Return the next rebase record from the file. If no more records, return None. """ lines = [] first_tag = '' while 1: line = self._uhandle.readline() if not line: break if line[:len( first_tag )] == first_tag: self._uhandle.saveline(line) break if not line: return None if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data class Dictionary: """Accesses a rebase file using a dictionary interface. """ __filename_key = '__filename' def __init__(self, indexname, parser=None): """__init__(self, indexname, parser=None) Open a Rebase Dictionary. indexname is the name of the index for the dictionary. The index should have been created using the index_file function. parser is an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. """ self._index = Index.Index(indexname) self._handle = open(self._index[Dictionary.__filename_key]) self._parser = parser def __len__(self): return len(self._index) def __getitem__(self, key): start, len = self._index[key] self._handle.seek(start) data = self._handle.read(len) if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __getattr__(self, name): return getattr(self._index, name) class RebaseParser( sgmllib.SGMLParser ): """Parses Rebase sequence data into a Record object. """ def reset(self): sgmllib.SGMLParser.reset( self ) self.text = '' self.enzyme_dict = UserDict.UserDict() self._state = 'title' self.key_waiting = '' self.enzyme_dict[ 'factoids' ] = [] self.enzyme_dict[ 'number_of_sites' ] = UserDict.UserDict() self._table_nest_level = 0 self._table_nest_dir = '' self._factoid = '' def parse(self, handle): self.reset() self.feed(handle) return self.enzyme_dict def feed(self, handle): """feed(self, handle ) Feed in rebase data for scanning. handle is a file-like object containing rebase data. consumer is a Consumer object that will receive events as the rebase data is scanned. """ if isinstance(handle, File.UndoHandle): uhandle = handle else: uhandle = File.UndoHandle(handle) text = '' while 1: line = uhandle.readline() line = string.strip( line ) if( is_blank_line( line, 0 ) ): break if( line[ -7: ] == '' ): break text = text + ' ' + line sgmllib.SGMLParser.feed( self, text ) def handle_data(self, newtext ): newtext = string.strip( newtext ) self.text = self.text + newtext def start_table( self, attrs ): self._table_nest_level = self._table_nest_level + 1 self._table_nest_dir = 'increasing' def end_table( self ): self._table_nest_level = self._table_nest_level - 1 if( self._table_nest_dir == 'increasing' ): if( self._state == 'details' ): self.extract_details() self._state = 'number_of_sites' elif( self._state == 'number_of_sites' ): self.extract_number_of_sites() self._state = 'complete' self._table_nest_dir = 'decreasing' def start_b( self, attrs ): if( self._state == 'details' ): self.extract_details() else: self.flush_text() def end_b( self ): if( self._state == 'details' ): text = self.flush_text() if( text != '' ): if( text[ -1 ] == ':' ): key = self.key_waiting if( key != '' ): self.enzyme_dict[ key ] = self._factoid self._factoid = '' self.key_waiting = text[ :-1 ] else: self._factoid = self._factoid + ' ' + text def start_i( self, attrs ): if( self._state == 'number_of_sites' ): self.extract_number_of_sites() def end_i( self ): if( self._state == 'details' ): self.extract_details() elif( self._state == 'number_of_sites' ): text = self.flush_text() if( text != '' ): if( text[ -1 ] == ':' ): self.key_waiting = text[ :-1 ] elif( self.key_waiting != '' ): key = self.key_waiting self.key_waiting = '' self.enzyme_dict[ 'number_of_sites' ][ key ] = text def start_pre( self, attrs ): self.flush_text() if( self._state == 'sequence' ): self._state = '5_to_3_strand' def end_pre( self ): if( self._state == '5_to_3_strand' ): text = self.flush_text() cols = string.split( text, '...' ) if( len( cols ) > 1 ): self.enzyme_dict[ '5_to_3_strand' ] = cols[ 1 ] self.enzyme_dict[ '3_to_5_strand' ] = '' self._state = 'details' elif( self._state == '3_to_5_strand' ): text = self.flush_text() self.enzyme_dict[ '3_to_5_strand' ] = text self._state = 'details' def do_br( self, attrs ): if( self._state == '5_to_3_strand' ): text = self.flush_text() if( text != '' ): self.enzyme_dict[ '5_to_3_strand' ] = text self._state = '3_to_5_strand' elif( self._state == 'details' ): self.extract_details() key = self.key_waiting if( self._factoid != '' ): if( key != '' ): self.enzyme_dict[ key ] = self._factoid self.key_waiting = '' else: self.enzyme_dict[ 'factoids' ].append( self._factoid ) self._factoid = '' def start_font( self, attrs ): self.flush_text() def end_font( self ): if( self._state == 'title' ): text = self.flush_text() if( text != '' ): self._state = 'descriptor' self.enzyme_dict[ 'title' ] = text elif( self._state == 'descriptor' ): text = self.flush_text() if( text != '' ): self._state = 'sequence' self.enzyme_dict[ 'descriptor' ] = text def extract_details( self ): text = self.flush_text() if( text != '' ): self._factoid = self._factoid + ' ' + text def extract_number_of_sites( self ): text = self.flush_text() if( text != '' ): key = self.key_waiting if( key != '' ): self.enzyme_dict[ 'number_of_sites' ][ key ] = text self.key_waiting = '' def flush_text( self ): text = string.strip( self.text[:] ) self.text = '' return text def print_item( self, item, level = 1 ): indent = ' ' for j in range( 0, level ): indent = indent + ' ' if( type( item ) == type( '' ) ): if( item != '' ): print '%s%s' % ( indent, item ) elif( type( item ) == type([])): for subitem in item: self.print_item( subitem, level + 1 ) elif( isinstance( item, UserDict.UserDict ) ): for subitem in item.keys(): print '%skey is %s' % ( indent, subitem ) self.print_item( item[ subitem ], level + 1 ) elif( type( item ) == type( {} ) ): for subitem in item.keys(): print '%skey is %s' % ( indent, subitem ) self.print_item( item[ subitem ], level + 1 ) else: print item def print_tags( self ): for key in self.enzyme_dict.keys(): print 'key %s' % key self.print_item( self.enzyme_dict[ key ] ) if( __name__ == '__main__' ): handle = open( 'bamii.htm') undo_handle = Bio.File.UndoHandle( handle ) rebase_parser = RebaseParser() rebase_parser.parse( handle ) rebase_parser.print_tags()