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import string
import sgmllib
import Bio.File
"""
The UniGene site is:
http://www.ncbi.nlm.nih.gov/UniGene/
"""
class Record( dict):
def __init__( self ):
dict.__init__( self )
def __str__( self ):
queue_keys = self.keys()
queue_keys.sort()
out = ''
for key in queue_keys:
out = out + 'key %s\n' % key
out = out + self.print_item( self[ key ] )
out = out + '\n'
return out
def print_item( self, item, level = 1 ):
indent = ' '
out = ''
for j in range( 0, level ):
indent = indent + ' '
if( type( item ) == type( '' ) ):
if( item != '' ):
out = out + '%s%s\n' % ( indent, item )
elif( type( item ) == type([])):
for subitem in item:
out = out + self.print_item( subitem, level + 1 )
elif( isinstance( item, dict ) ):
keys = item.keys()
keys.sort()
for subitem in keys:
out = out + '%skey is %s\n' % ( indent, subitem )
out = out + self.print_item( item[ subitem ], level + 1 )
else:
out = out + '%s\n' % str( item )
return out
class UniGeneParser( sgmllib.SGMLParser ):
def reset( self ):
sgmllib.SGMLParser.reset( self )
self.text = ''
self.queue = Record()
self.open_tag_stack = []
self.open_tag = 'open_html'
self.key_waiting = ''
self.master_key = ''
self.context = 'general_info'
def parse( self, handle ):
self.reset()
self.feed( handle )
for key in self.queue.keys():
if( self.queue[ key ] == {} ):
if( key[ :15 ] == 'UniGene Cluster' ):
self.queue[ 'UniGene Cluster' ] = key[ 16: ]
del self.queue[ key ]
return self.queue
#
# Assumes an empty line between records
#
def feed( self, handle ):
if isinstance(handle, Bio.File.UndoHandle):
uhandle = handle
else:
uhandle = Bio.File.UndoHandle(handle)
text = ''
while 1:
line = uhandle.readline()
line = string.strip( line )
if( line == '' ):
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_a( self, attrs ):
if( self.context == 'seq_info' ):
if( self.open_tag != 'open_b' ):
self.text = ''
# self.queue.append( attrs )
def end_a( self ):
if( self.context == 'seq_info' ):
if( self.open_tag != 'open_b' ):
if( self.key_waiting == '' ):
self.key_waiting = self.text
self.text = ''
def start_b( self, attrs ):
self.open_tag_stack.append( self.open_tag )
self.open_tag = 'open_b'
if( self.key_waiting == '' ):
self.text = ''
def end_b( self ):
if( self.text[ :15 ] == 'UniGene Cluster' ):
self.queue[ 'UniGene Cluster' ] = self.text[ 16: ]
self.text = ''
elif( self.key_waiting == '' ):
self.extract_key()
def extract_key( self ):
text = string.strip( self.text )
key = string.join( string.split( text ) )
words = string.split( key )
key = string.join( words[ :2 ] )
self.text = ''
try:
self.open_tag = self.open_tag_stack.pop()
except:
self.open_tag = 'open_html'
if( self.open_tag == 'open_table_data' ):
if( self.context == 'general_info' ):
if( self.key_waiting == '' ):
self.key_waiting = key
self.text = ''
elif( self.context == 'seq_info' ):
if( text == 'Key to Symbols' ):
self.context = 'legend'
self.master_key = key
elif( self.context == 'general_info' ):
self.master_key = key
if( string.find( key, 'SEQUENCE' ) != -1 ):
self.context = 'seq_info'
self.queue[ key ] = dict()
elif( self.context == 'seq_info' ):
self.queue[ key ] = dict()
self.master_key = key
def start_table( self, attrs ):
self.open_tag_stack.append( self.open_tag )
self.open_tag = 'open_table'
def end_table( self ):
try:
self.open_tag = self.open_tag_stack.pop()
except:
self.open_tag = 'open_html'
self.key_waiting = ''
def start_tr( self, attrs ):
self.open_tag_stack.append( self.open_tag )
self.open_tag = 'open_table_row'
self.text = ''
def end_tr( self ):
try:
self.open_tag = self.open_tag_stack.pop()
except:
self.open_tag = 'open_html'
text = self.text
if text:
self.text = ''
if( text[ 0 ] == ':' ):
text = text[ 1: ]
text = string.join( string.split( text ) )
if( ( self.context == 'general_info' ) or \
( self.context == 'seq_info' ) ):
try:
contents = self.queue[ self.master_key ][ self.key_waiting ]
if( type( contents ) == type( [] ) ):
contents.append( text )
else:
self.queue[ self.master_key ][ self.key_waiting ] = \
[ contents , text ]
except:
self.queue[ self.master_key ][ self.key_waiting ] = text
self.key_waiting = ''
def start_td( self, attrs ):
self.open_tag_stack.append( self.open_tag )
self.open_tag = 'open_table_data'
def end_td( self ):
try:
self.open_tag = self.open_tag_stack.pop()
except:
self.open_tag = 'open_html'
if( self.context == 'seq_info' ):
self.text = self.text + ' '
if( __name__ == '__main__' ):
handle = open( 'Hs13225.htm')
undo_handle = Bio.File.UndoHandle( handle )
unigene_parser = UniGeneParser()
record = unigene_parser.parse( handle )
print record
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