Debug the reading of gziped files, change the doc of obipr2 and obisilva

distutils.ext/obidistutils/serenity/checkpip.py

@@ -56,41 +56,13 @@ def get_a_pip_module(minversion=PIP_MINVERSION):
     tmpdir = get_serenity_dir()
     
     if not local_pip:    
-#        if not is_pip_installed(minversion):
-#             try:
-#                 if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
-#                     os.environ['https_proxy']=os.environ['http_proxy']
-#                 pipinstallscript = urllib2.urlopen('https://bootstrap.pypa.io/get-pip.py')
-#             except:
-#                 raise DistutilsError,"Pip (>=%s) is not install on your system and I cannot install it" % PIP_MINVERSION
-#             
-#             script = pipinstallscript.read()
-#             getpip_py = os.path.join(tmpdir, "get-pip.py")
-#             with open(getpip_py, "wb") as fp:
-#                 log.info("Downloading temporary pip...")
-#                 fp.write(script)
-#                 log.info("   done.")
-#                 
-#             getpip = imp.load_source("getpip",getpip_py)
-#             ZIPFILE=getpip.ZIPFILE
-#     
-#             pip_zip = os.path.join(tmpdir, "pip.zip")
-#             with open(pip_zip, "wb") as fp:
-#                 log.info("Installing temporary pip...")
-#                 fp.write(base64.decodestring(ZIPFILE))
-#                 log.info("   done.")
-#                 
-#             # Add the zipfile to sys.path so that we can import it
-#             sys.path.insert(0,pip_zip)
-#             zi = zipimport.zipimporter(pip_zip)
-#             pip = zi.load_module("pip") 
-#            pip = importlib.import_module('obidistutils.serenity.pip')
-#        else:
         serenity = importlib.import_module('obidistutils.serenity')
         sys.path.insert(0, os.path.dirname(serenity.__file__))
         pip = importlib.import_module('pip')
 
         local_pip.append(pip)
+    else:
+        pip = local_pip[-1]
     
     # Prepare the CERT certificat for https download
             

sample/CAA64141.fasta

->CAA64141 taxid=4932; unnamed protein product [Saccharomyces cerevisiae]
-MGVSANLFVKQRGSTTALKQPKEIGFYSRTKDEEYLISDDTNLNYYYLPDAELDRKLDLS
-SGFQKFKDYYKDFEDRCSLRGLLETIESSERHKGKKINADIITFRGIARKLISCAFDSPS
-FNTVDLRIVSFNGQLFIKEVPEAVNAAKASSATEAGRNINQDLNVFTGYKFETLATLSNP
-LQYTPREVIEKRTKRIVSHGDEYISVVRTGVGNCKLILGAEVDCIFDFKENGRDNLKHYA
-ELKCTQQVANISDTHKFERKLFRTWLQCFLVGIPRIIYGFKDDHYVLKTVEEFSTEEVPV
-LLKNNNPQVGSACLEAIKWYGLLTEWLLKMIPRDEDPHSQIRAFKLVFENNHLRLSEIEE
-SDEEYSGLIDGEHILSNGFKEWRKSLK

setup.py

@@ -19,7 +19,7 @@ from os import path
 
 
 PACKAGE = "OBITools"
-VERSION = "1.1.4"
+VERSION = "1.1.5"
 AUTHOR  = 'Eric Coissac'
 EMAIL   = 'eric@coissac.eu'
 URL     = 'metabarcoding.org/obitools'

src/obipr2.py

 #!/usr/local/bin/python
 '''
-:py:mod:`obipr2`: manages taxonomic databases
-==================================================
+:py:mod:`obipr2`: converts silva database into an ecoPCR database
+=================================================================
 
 :py:mod:`obipr2`: converts and optionally download the `PR2 database <http://ssu-rrna.org/pr2/>`_
 into an ecoPCR database. The formated database include the taxonomy as defined by the PR2 authors.
 
 .. warning::
-    Take care that the numeric taxids associated to the sequences are internal 
+    Take care that the numeric taxids associated to the sequences are specific 
     to this **PR2** database and not compatible with the NCBI taxids. 
     The taxids present in a version of the **PR2** database are are just valid for 
     this version of the database and not compatible with the taxids used in another version

src/obisilva.py

@@ -7,7 +7,7 @@
 into an ecoPCR database. The formated database include the taxonomy as defined by the Silva authors.
 
 .. warning::
-    Take care that the numeric taxids associated to the sequences are internal 
+    Take care that the numeric taxids associated to the sequences are specific 
     to this Silva database and not compatible with the NCBI taxids. 
     The taxids present in a version of the Silva database (*i.e* ssu, lsu, parc, ref...)
     are are just valid for this version of the database and not compatible 
@@ -140,6 +140,7 @@ def getHyperlink(url):
     return links
     
 def silvaURLS(options):
+    global siteurl
     
     if options.local is not None:
         archive = dict((f,f) for f in listdir(options.local) if isfile(join(options.local,f)))
@@ -192,7 +193,6 @@ def silvaURLS(options):
                                      {True:"nr_" ,   False:""}[options.nr],
                                      {True:"trunc" , False:"full"}[options.trunc]
                                     )
-           
     return "%s/%s" %(siteurl,sequrl),"%s/%s" %(siteurl,taxurl),output
     
     

src/obitools/options/__init__.py

@@ -17,12 +17,13 @@ from obitools.format.options import addInputFormatOption, addInOutputOption,\
     autoEntriesIterator
 import time
     
-from _options import fileWithProgressBar, \
-                     currentInputFileName, \
-                     currentInputFile, \
-                     currentFileSize, \
-                     currentFileTell, \
-                     allEntryIterator
+from _options import fileWithProgressBar        # @UnresolvedImport 
+from _options import currentInputFileName       # @UnresolvedImport 
+from _options import currentInputFile           # @UnresolvedImport 
+from _options import currentFileSize            # @UnresolvedImport 
+from _options import currentFileTell            # @UnresolvedImport 
+from _options import allEntryIterator           # @UnresolvedImport
+
 from obitools.ecopcr.sequence import EcoPCRDBSequenceIterator
 
 class ObiHelpFormatter (IndentedHelpFormatter):

src/obitools/options/_options.pyx

@@ -84,7 +84,7 @@ def allEntryIterator(files,entryIterator,with_progress=False,histo_step=102,opti
                     cfs.currentFileSize=fileSize(cfs.currentFile)
                     debug(f)
                 
-                    if with_progress:
+                    if with_progress and cfs.currentFileSize >0:
                         f=fileWithProgressBar(f,step=histo_step)           
                     
             if entryIterator is None:

src/obitools/utils/__init__.py

@@ -12,8 +12,8 @@ from obitools.gzip import GzipFile
 from obitools.zipfile import ZipFile
 import os.path
 
-from _utils import FakeFile
-from _utils import progressBar
+from _utils import FakeFile     # @UnresolvedImport
+from _utils import progressBar  # @UnresolvedImport
 import zlib
 
 try:
@@ -97,9 +97,11 @@ def universalTell(file):
     @return: position in the file
     @rtype:  C{int}
     '''
-    if isinstance(file, GzipFile):
-        file=file.myfileobj
-    return file.tell()
+    
+    if hasattr(file, "tell"):
+        return file.tell()
+    else:
+        return None
 
 def fileSize(file):
     '''
@@ -112,12 +114,13 @@ def fileSize(file):
     @return: the size of the file
     @rtype: C{int}
     '''
-    if isinstance(file, GzipFile):
-        file=file.myfileobj
-    pos = file.tell()
-    file.seek(0,2)
-    length = file.tell()
-    file.seek(pos,0)
+    if hasattr(file, "tell"):
+        pos = file.tell()
+        file.seek(0,2)
+        length = file.tell()
+        file.seek(pos,0)
+    else:
+        length=0
     return length
 
 

src/obitools/utils/_utils.pyx

@@ -40,7 +40,7 @@ cdef class FakeFile:
         
     cpdef str readline(self):
      
-            cdef str line
+            cdef str line  # @DuplicatedSignature
             
             try:
                 if self.__buffer:

src/obitools/version.py

 major = 1
 minor = 1
-serial= '4'
+serial= '5'
 
 version = "%2d.%02d %s" % (major,minor,serial)