Patch to fit the version 0.20 of cython

src/obitools/_obitools.pyx

@@ -81,7 +81,7 @@ cdef class BioSequence(object):
         self._seq=seq
         self._info = dict(info)
         if rawinfo is not None:
-            self.__rawinfo=' ' + rawinfo
+            self.__rawinfo=b' ' + rawinfo
         else:
             self.__rawinfo=None
         self._rawparser=rawparser
@@ -221,7 +221,7 @@ cdef class BioSequence(object):
             m = p.search(self.__rawinfo)
             if m is not None:
                 v=m.group(1)
-                self.__rawinfo=' ' + self.__rawinfo[0:m.start(0)]+self.__rawinfo[m.end(0):]
+                self.__rawinfo=b' ' + self.__rawinfo[0:m.start(0)]+self.__rawinfo[m.end(0):]
                 try:
                     v = eval(v)
                 except:
@@ -301,7 +301,7 @@ cdef class BioSequence(object):
             m = p.search(self.__rawinfo)
             if m is not None:
                 v=m.group(1)
-                self.__rawinfo=' ' + self.__rawinfo[0:m.start(0)]+self.__rawinfo[m.end(0):]
+                self.__rawinfo=b' ' + self.__rawinfo[0:m.start(0)]+self.__rawinfo[m.end(0):]
                 try:
                     v = eval(v)
                 except:
@@ -640,7 +640,7 @@ cdef class SubSequence(WrappedBioSequence):
         return len(self._xrange)
     
     cpdef bytes getStr(self):
-        return ''.join([x for x in self])
+        return b''.join([x for x in self])
     
     def __iter__(self):
         return (self.wrapped.getSymbolAt(x) for x in self._xrange)
@@ -651,11 +651,11 @@ cdef class SubSequence(WrappedBioSequence):
     
     id = property(getId,setId, None)
 
-cdef dict _comp={'a': 't', 'c': 'g', 'g': 'c', 't': 'a',
-                 'r': 'y', 'y': 'r', 'k': 'm', 'm': 'k', 
-                 's': 's', 'w': 'w', 'b': 'v', 'd': 'h', 
-                 'h': 'd', 'v': 'b', 'n': 'n', 'u': 'a',
-                 '-': '-'}
+cdef dict _comp={b'a': b't', b'c': b'g', b'g': b'c', b't': b'a',
+                 b'r': b'y', b'y': b'r', b'k': b'm', b'm': b'k', 
+                 b's': b's', b'w': b'w', b'b': b'v', b'd': b'h', 
+                 b'h': b'd', b'v': b'b', b'n': b'n', b'u': b'a',
+                 b'-': b'-'}
 
 
 cdef class DNAComplementSequence(WrappedBioSequence):
@@ -693,7 +693,7 @@ cdef class DNAComplementSequence(WrappedBioSequence):
         return len(self._wrapped)
     
     cpdef bytes getStr(self):
-        return ''.join([x for x in self])
+        return b''.join([x for x in self])
     
     def __iter__(self):
         return (self.getSymbolAt(x) for x in xrange(len(self)))
@@ -714,16 +714,16 @@ cdef class DNAComplementSequence(WrappedBioSequence):
     
     id = property(getId,setId, None)
                 
-cdef set _iupac=set(['r', 'y', 'k', 'm', 
-                     's', 'w', 'b', 'd', 
-                     'h', 'v', 'n',
-                     'R', 'Y', 'K', 'M', 
-                     'S', 'W', 'B', 'D', 
-                     'H', 'V', 'N'])
+cdef set _iupac=set([b'r', b'y', b'k', b'm', 
+                     b's', b'w', b'b', b'd', 
+                     b'h', b'v', b'n',
+                     b'R', b'Y', b'K', b'M', 
+                     b'S', b'W', b'B', b'D', 
+                     b'H', b'V', b'N'])
 
 #cdef char *_iupac=b"acgtrykmswbdhvnu-"
 
-cdef set _nuc = set(['a', 'c', 'g', 't','u','A', 'C', 'G', 'T','U','-'])
+cdef set _nuc = set([b'a', b'c', b'g', b't',b'u',b'A', b'C', b'G', b'T',b'U',b'-'])
 
 #cdef char *_nuc=b"acgt-"
 

src/obitools/fastq/_fastq.pyx

@@ -214,7 +214,7 @@ cpdef bytes formatFastq(object data, bint gbmode=False, bint upper=False):
         id = sequence.id
         if gbmode:
             if b'gi' in sequence:
-                id = b"gi|%s|%s" % (sequence[b'gi'],id)
+                id = bytes(b"gi|%s|%s" % (sequence[b'gi'],id))
             else:
                 id = b"lcl|%s|" % (id)
         if hasattr(sequence, b"quality"):