Bug fixes for input handlers, openers, parsers etc. Compiling but not

tested

python/obitools3/parsers/fastq.pyx

@@ -6,11 +6,14 @@ Created on 30 mars 2016
 @author: coissac
 '''
 
+from obitools3.dms.obiseq import Nuc_Seq
+
+
 def fastqIterator(lineiterator, 
                   int skip=0,
                   only=None,
                   int qualityoffset=-1,
-                  bool noquality=False,
+                  bint noquality=False,
                   firstline=None,
                   int buffersize=100000000
                  ):

python/obitools3/parsers/universal.pxd

@@ -0,0 +1,7 @@
+#cython: language_level=3
+
+from ..utils cimport str2bytes
+
+from ..files.universalopener cimport uopen
+from ..files.linebuffer cimport LineBuffer
+from obitools3.dms.obiseq cimport Nuc_Seq

python/obitools3/uri/decode.pxd

@@ -0,0 +1,6 @@
+#cython: language_level=3
+
+from obitools3.dms.dms cimport DMS
+from obitools3.dms.view.view cimport View
+from obitools3.dms.column.column cimport Column
+from obitools3.dms.taxo.taxo cimport Taxonomy

python/obitools3/uri/decode.pyx

@@ -1,12 +1,11 @@
-from urllib.parse import urlparse, parse_qs, ParseResultBytes
+#cython: language_level=3
+
+from urllib.parse import urlparse, urlunparse, parse_qs, ParseResultBytes
 from os.path import isdir, isfile, basename, join
 
 from obitools3.utils import tobytes
 
 from obitools3.dms.dms import DMS
-from obitools3.dms.view.view import View
-from obitools3.dms.column.column import Column
-from obitools3.dms.taxo import Taxonomy
 
 from obitools3.files.universalopener import uopen
 from obitools3.parsers.fasta import fastaNucIterator
@@ -15,7 +14,7 @@ from obitools3.parsers.universal import entryIteratorFactory
 
 from obitools3.dms.obiseq import Nuc_Seq
 
-cdef class MalformedURIException(RuntimeError):
+class MalformedURIException(RuntimeError):
     pass
 
 cdef open_dms(bytes path,create=False):
@@ -30,10 +29,10 @@ cdef open_dms(bytes path,create=False):
     while(pos>0):
         pos = path.find(b"/",pos)
         if pos>0:
-            dirpath=path[0:pos]
+            dmspath=path[0:pos]
         else:
-            dirpath=path
+            dmspath=path
-        if not isdir(dirpath):
+        if not isdir(dmspath):
             dmsdirname=dmspath+b".obidms"
             if isdir(dmsdirname):
                 dmsname=basename(dmspath)
@@ -70,7 +69,7 @@ def open_dms_element(DMS dms, bytes path):
             if len(path_parts) == 2:
                 taxon=taxo[int(path_parts[2])]
                 return (dms,taxon)
-            elif (len(path_parts) > 2:
+            elif len(path_parts) > 2:
                 raise MalformedURIException('Malformed Taxonomy URI')
             return (dms,taxo)
 
@@ -148,7 +147,7 @@ def open_uri(uri,input=True,config={}):
         scheme=b'file'
         dms = open_dms(urip.path)
         if dms is None and default_dms is not None:
-            dms=(default_dms,urip.path))
+            dms=(default_dms,urip.path)
            
         
         if dms is not None:
@@ -198,7 +197,7 @@ def open_uri(uri,input=True,config={}):
             seqtype=config["obi"]["seqtype"]
         
         if b'skip' in qualifiers:
-            skip=int(qualifiers[b"skip"][0]
+            skip=int(qualifiers[b"skip"][0])
         else:
             skip=config["obi"]["skeep"]
         if skip < 0:    
@@ -290,16 +289,16 @@ def open_uri(uri,input=True,config={}):
             raise MalformedURIException('Malformed blanklineskip argument in URI')
         
         if b"commentchar" in qualifiers:
-            nastring=qualifiers[b"commentchar"][0][0]
+            commentchar=qualifiers[b"commentchar"][0][0]
         else:
-            nastring=config["obi"]["commentchar"]
+            commentchar=config["obi"]["commentchar"]
 
         if format is not None:
             if qualifiers[b"seqtype"]==b"nuc":
                 objclass = Nuc_Seq
-                if format="fasta":
+                if format==b"fasta":
                     iseq = fastaNucIterator(file,skip,only)
-                elif format="fastq":
+                elif format==b"fastq":
                     iseq = fastqIterator(file,
                                          skip,only,
                                          offset,
@@ -309,7 +308,7 @@ def open_uri(uri,input=True,config={}):
             elif qualifiers[b"seqtype"]==b"prot":
                 raise NotImplementedError()
         else:
-            iseq,objclass = entryIterator(file,
+            iseq,objclass = entryIteratorFactory(file,
                                           skip,only,
                                           seqtype,
                                           offset,