Fixed stdout output

versions of python

python/obitools3/dms/taxo/taxo.pyx

@@ -325,8 +325,9 @@ cdef class Taxonomy(OBIWrapper) :
         cdef Taxon taxon
         try:
             taxon = self.get_taxon_by_taxid(taxid)
-        except:
+        except Exception as e:
-            raise StopIteration
+            print('\n'+e, file=sys.stderr)
+            return 
         if taxon is not None:
             while taxon.taxid != 1:
                 yield taxon
@@ -334,7 +335,7 @@ cdef class Taxonomy(OBIWrapper) :
                 taxon = taxon.parent
             yield taxon
         else:
-            raise StopIteration
+            return
 
 
     def is_ancestor(self, int ancestor_taxid, int taxid):

python/obitools3/format/tab.pyx

@@ -23,16 +23,17 @@ cdef class TabFormat:
     @cython.boundscheck(False)    
     def __call__(self, object data):
         
-        cdef set ktags
+        cdef object ktags
         cdef list tags = [key for key in data]
         
         line = []
-        
+        if self.tags != None and self.tags:
-        if self.tags is not None and self.tags:
+            ktags = list(self.tags)
-            ktags = self.tags
         else:
-            ktags = set(tags)            
+            ktags = list(set(tags))   
-                
+                     
+        ktags.sort()
+                        
         if self.header and self.first_line:
             for k in ktags:
                 if k in tags:

python/obitools3/parsers/fastq.pyx

@@ -103,7 +103,11 @@ def fastqWithQualityIterator(lineiterator,
         yield seq
 
         read+=1
-        hline = next(i)
+        try:
+            hline = next(i)
+        except StopIteration:
+            return
+
     
 
 def fastqWithoutQualityIterator(lineiterator, 
@@ -174,5 +178,7 @@ def fastqWithoutQualityIterator(lineiterator,
         yield seq
     
         read+=1
-        hline = next(i)
+        try:
-        
+            hline = next(i)
+        except StopIteration:
+            return        

python/obitools3/parsers/tab.pyx

@@ -99,7 +99,10 @@ def tabIterator(lineiterator,
         
         read+=1
         
-        line = next(iterator)
+        try:
+            line = next(iterator)
+        except StopIteration:
+            return 
     
         
         

python/obitools3/uri/decode.pyx

@@ -280,7 +280,7 @@ def open_uri(uri,
             iseq = urib
             objclass = bytes
     else:  # TODO update uopen to be able to write? 
-        if config['obi']['outputformat'] == b'metabaR':
+        if 'outputformat' in config['obi'] and config['obi']['outputformat'] == b'metabaR':
             if 'metabarprefix' not in config['obi']:
                 raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
             else:

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b24'
+serial= '1b26'
 
 version ="%d.%d.%s" % (major,minor,serial)