*** empty log message ***

Bio/UniGene/__init__.py

@@ -6,7 +6,6 @@
 import Bio.File
 import Martel
 from mx import TextTools
-import unigene_format
 
 
 
@@ -16,10 +15,10 @@ def reset( self ):
         sgmllib.SGMLParser.reset( self )
         self.text = ''
         self.queue = UserDict.UserDict()
-        self.taglist = []
-        self.tag = 'html'
-        self.nextkey = ''
-        self.table = ''
+        self.open_tag_stack = []
+        self.open_tag = 'open_html'
+        self.key_waiting = ''
+        self.master_key = ''
         self.context = 'general_info'
 
     def parse( self, handle ):
@@ -43,9 +42,11 @@ def feed( self, handle ):
         text = ''
         while 1:
             line = uhandle.readline()
-            if( string.strip( line ) == '' ):
+            line = string.strip( line )
+            if( line == '' ):
                 break
-            text = text + line
+            text = text + ' ' + line
+
         sgmllib.SGMLParser.feed( self, text )
 
 
@@ -56,122 +57,146 @@ def handle_data(self, newtext ):
 
     def start_a( self, attrs ):
         if( self.context == 'seq_info' ):
-            self.text = ''
+            if( self.open_tag != 'open_b' ):
+                self.text = ''
 
 #        self.queue.append( attrs )
 
     def end_a( self ):
         if( self.context == 'seq_info' ):
-            self.nextkey = self.text
-            self.text = ''
+            if( self.open_tag != 'open_b' ):
+                if( self.key_waiting == '' ):
+                    self.key_waiting = self.text
+                    self.text = ''
 
     def start_b( self, attrs ):
 
-        self.taglist.append( self.tag )
-        self.tag = 'label'
-        self.text = ''
+        self.open_tag_stack.append( self.open_tag )
+        self.open_tag = 'open_b'
+        if( self.key_waiting == '' ):
+            self.text = ''
 
     def end_b( self ):
-        key = string.strip( self.text )
+        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.tag = self.taglist.pop()
+            self.open_tag = self.open_tag_stack.pop()
         except:
-            self.tag = 'html'
-        if( self.tag == 'table_data' ):
+            self.open_tag = 'open_html'
+        if( self.open_tag == 'open_table_data' ):
             if( self.context == 'general_info' ):
-                self.nextkey = key
-                self.text = ''
+                if( self.key_waiting == '' ):
+                    self.key_waiting = key
+                    self.text = ''
             elif( self.context == 'seq_info' ):
-                if( key == 'Key to Symbols' ):
+                if( text == 'Key to Symbols' ):
                     self.context = 'legend'
-                    self.table = key
+                    self.master_key = key
         elif( self.context == 'general_info' ):
-            self.table = key
+            self.master_key = key
             if( string.find( key, 'SEQUENCE' ) != -1 ):
                 self.context = 'seq_info'
             self.queue[ key ] = UserDict.UserDict()
         elif( self.context == 'seq_info' ):
             self.queue[ key ] = UserDict.UserDict()
-            self.table = key
+            self.master_key = key
 
 
 
     def start_table( self, attrs ):
-        self.taglist.append( self.tag )
-        self.tag = 'table'
+        self.open_tag_stack.append( self.open_tag )
+        self.open_tag = 'open_table'
 
     def end_table( self ):
         try:
-            self.tag = self.taglist.pop()
+            self.open_tag = self.open_tag_stack.pop()
         except:
-            self.tag = 'html'
+            self.open_tag = 'open_html'
+        self.key_waiting = ''
 
     def start_tr( self, attrs ):
-        self.taglist.append( self.tag )
-        self.tag = 'table_row'
+        self.open_tag_stack.append( self.open_tag )
+        self.open_tag = 'open_table_row'
         self.text = ''
 
     def end_tr( self ):
         try:
-            self.tag = self.taglist.pop()
+            self.open_tag = self.open_tag_stack.pop()
         except:
-            self.tag = 'html'
+            self.open_tag = 'open_html'
         text = self.text
-        self.text = ''
-        if( text[ 0 ] == ':' ):
-            text = text[ 1: ]
-        if( self.context == 'general_info' ):
-            self.queue[ self.table ][ self.nextkey ] = text
-        elif( self.context == 'seq_info' ):
-            self.queue[ self.table ][ self.nextkey ] = 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.taglist.append( self.tag )
-        self.tag = 'table_data'
+        self.open_tag_stack.append( self.open_tag )
+        self.open_tag = 'open_table_data'
 
     def end_td( self ):
         try:
-            self.tag = self.taglist.pop()
+            self.open_tag = self.open_tag_stack.pop()
         except:
-            self.tag = 'html'
+            self.open_tag = 'open_html'
         if( self.context == 'seq_info' ):
             self.text = self.text + ' '
 
-    def print_item( self, item ):
+    def print_item( self, item, level = 1 ):
+        indent = '    '
+        for j in range( 0, level ):
+            indent = indent + '    '
         if( type( item ) == type( '' ) ):
             if( item != '' ):
-                print item
-        elif( type( item ) == type( [] ) ):
+                print '%s%s' % ( indent, item )
+        elif( type( item ) == type([])):
             for subitem in item:
-                self.print_item( subitem )
-        elif( type( item ) == type( {} ) ):
+                self.print_item( subitem, level + 1 )
+        elif( isinstance( item, UserDict.UserDict ) ):
             for subitem in item.keys():
-                self.print_item( subitem )
-                self.print_item( item[ subitem ] )
+                print '%skey is %s' % ( indent, subitem )
+                self.print_item( item[ subitem ], level + 1 )
         else:
             print item
 
     def print_tags( self ):
-        print '\nTAGS\n'
         for key in self.queue.keys():
-            print key
+            print 'key %s' % key
             self.print_item( self.queue[ key ] )
 
-    def join_tags( self ):
-        self.data = '\n'.join( self.queue ) + '\n'
-        print self.data
 
 
 if( __name__ == '__main__' ):
-    handle = urllib.urlopen( 'http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=222015&OPT=text')
+    handle = open( 'Hs13225.htm')
     undo_handle = Bio.File.UndoHandle( handle )
     unigene_parser = UniGeneParser()
     unigene_parser.parse( handle )
     unigene_parser.print_tags()
-#    unigene_parser.print_data()
-
-

Tests/output/test_unigene

@@ -1,5 +1,4 @@
 test_unigene
-Warning: can't open .\output\test_unigene
 testing Bt145.htm
 key EXPRESSION INFORMATION
         key is Note
@@ -91,61 +90,24 @@ key EST SEQUENCES
             cDNA clone IMAGE:574684 5' read
 
 
-testing Dr48.htm
+testing Rn35.htm
 key EXPRESSION INFORMATION
         key is cDNA sources
-            heart, kidney
+            Whole embryo
+key UniGene Cluster
+        Rn.35
 key SEE ALSO
-        key is LocusLink
-            30675
         key is HomoloGene
-            Dr.48
-key MAPPING INFORMATION
-        key is Chromosome
-            LG 10
-key mRNA/GENE SEQUENCES
-        key is L77146
-            Danio rerio heat shock cognate (hsc70) mRNA, complete cds
-        key is Y11413
-            D.rerio hsc70 mRNA
-key UniGene Cluster
-        Dr.48
+            Rn.35
 key EST SEQUENCES
-        key is AI313707
-            cDNA clone ZAE39 3' read
-        key is AW116799
-            cDNA clone 2601688 3' read
-        key is AI331807
-            cDNA clone (no-name) 3' read
-        key is AI385065
-            cDNA clone (no-name) 3' read
-        key is AW232778
-            cDNA clone (no-name) 3' read
-        key is AI667629
-            cDNA clone 2351498 3' read
-        key is AW077180
-            cDNA clone (no-name) 3' read
-        key is AA658601
-            cDNA clone zbr1406 kidney 3' read
-        key is AW233742
-            cDNA clone (no-name) 3' read
-        key is AI330589
-            cDNA clone (no-name) 3' read
-key SELECTED MODEL
-        key is M. musculus
-            SP:P08109- HS7C_MOUSE HEAT SHOCK COGNATE 71 KDA PROTEIN
93 % / 648 aa
-        key is C. elegans
-            PID:g3924750- similar to HSP-1 heat shock 70kd protein A83 % / 648 aa
-        key is D. melanogaster
-            SP:P11147- HS7D_DROME HEAT SHOCK 70 KDA PROTEIN COGNATE 483 % / 648 aa
-        key is S. cerevisiae
-            PID:g349747- Ssa1p: Heat shock protein of HSP70 family73 % / 648 aa
-        key is E. coli
-            PID:g1786196- chaperone Hsp7050 % / 566 aa
-        key is R. norvegicus
-            SP:P08109- HS7C_MOUSE HEAT SHOCK COGNATE 71 KDA PROTEIN
93 % / 648 aa
-        key is H. sapiens
-            SP:P11142- HS7C_HUMAN HEAT SHOCK COGNATE 71 KD PROTEIN
93 % / 648 aa
+        key is AA859652
+            cDNA clone UI-R-E0-bs-b-06-0-UI Whole embryo 3' read
+        key is BF547995
+            cDNA clone UI-R-E0-bs-b-06-0-UI Whole embryo 5' read
+        key is BE098081
+            cDNA clone UI-R-BJ1-asw-f-07-0-UI 3' read
+        key is BE101172
+            cDNA clone UI-R-BJ1-auh-h-09-0-UI 3' read
 
 
 testing Rn20.htm
@@ -333,4 +295,3 @@ key EST SEQUENCES
             cDNA clone IMAGE:223702 Eye 5' read 2.6 kb
 
 
-1 test OK.