Add patch in to eliminate sequence without taxonomic data

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@9 60f365c0-8329-0410-b2a4-ec073aeeaa1d

tools/ecoPCRFormat.py

@@ -249,7 +249,10 @@ def genbankParser(entry):
     Id = _gbParseID.findall(entry)[0]
     De = ' '.join(_gbParseDE.findall(entry)[0].split())
     Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
-    Tx = int(_gbParseTX.findall(entry)[0])
+    try:
+        Tx = int(_gbParseTX.findall(entry)[0])
+    except IndexError:
+        Tx = None
     return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
 
 def sequenceIterator(file,parser):
@@ -354,15 +357,18 @@ def ecoSeqWriter(file,input,taxindex,parser=genbankParser):
     
     progressBar(1, inputsize,reset=True)
     for entry in entries:
-        entry['taxid']=taxindex[entry['taxid']]
         if entry['taxid'] is not None:
-            seqcount+=1
-            output.write(ecoSeqPacker(entry))
+            entry['taxid']=taxindex[entry['taxid']]
+            if entry['taxid'] is not None:
+                seqcount+=1
+                output.write(ecoSeqPacker(entry))
+            else:
+                skipped.append[entry['id']]
+            where = universalTell(input)
+            progressBar(where, inputsize)
+            print >>sys.stderr," Readed sequences : %d     " % seqcount,
         else:
             skipped.append[entry['id']]
-        where = universalTell(input)
-        progressBar(where, inputsize)
-        print >>sys.stderr," Read sequences : %d     " % seqcount,
         
     print >>sys.stderr
     output.seek(0,0)