Patch several bugs or inconsistencies following the tutorial at Anthony's lab

.pydevproject

@@ -1,11 +1,9 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?eclipse-pydev version="1.0"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
-
-<pydev_project>
 <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
 <path>/OBITools-1.0/src</path>
 <path>/OBITools-1.0/textwrangler</path>
 </pydev_pathproperty>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python2.7</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python-2.7</pydev_property>
 </pydev_project>

doc/sphinx/source/optionsSet/outputformat.txt

@@ -17,7 +17,7 @@ Standard output format
 Generating an ecoPCR database
 .............................
 
-.. cmdoption::  --ecopcrDB-output=<PREFIX_FILENAME> 
+.. cmdoption::  --ecopcrdb-output=<PREFIX_FILENAME> 
 
       Creates an ecoPCR database from sequence records results
 

setup.py

@@ -6,9 +6,16 @@
 
 
 try:
-   from setuptools.core import setup
+    from setuptools import setup
 except ImportError:
-   from distutils.core import setup
+    import ez_setup
+    ez_setup.use_setuptools()
+    from setuptools import setup
+    
+# try:
+#    from setuptools.core import setup
+# except ImportError:
+#    from distutils.core import setup
 from distutils.extension import Extension
 from distutils.util import convert_path
 from distutils import log
@@ -39,6 +46,10 @@ import glob
 
 from os import path
 
+# requires = ['Cython>=0.20', 'Sphinx>=1.2']
+requires = ['Cython>=0.20']
+
+
 class install_scripts(ori_install_scripts):
 
     def remove_deprecated_script(self):
@@ -209,7 +220,7 @@ def findC(root,base=None,pyrexs=None):
 #from obitools.version import version as obiversion
 #sys.path.pop(0)
 
-VERSION =  "1.0.beta"
+VERSION =  "1.0.beta.2"
 AUTHOR  = 'Eric Coissac'
 EMAIL   = 'eric@coissac.eu'
 URL     = 'www.grenoble.prabi.fr/trac/OBITools'
@@ -242,6 +253,18 @@ else:
 
 setup(name="OBITools",
       description="Scripts and library for sequence analysis",
+      classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Intended Audience :: Research',
+        'License :: CeCILL-V2',
+        'Operating System :: Unix like',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 2',
+        'Topic :: NGS Data processing',
+        'Topic :: DNA metabarcoding',
+        'Topic :: Utilities',
+      ],
       version=VERSION,
       author=AUTHOR,
       author_email=EMAIL,
@@ -251,7 +274,7 @@ setup(name="OBITools",
       package_dir = {'': SRC},
       packages=findPackage(SRC),
       cmdclass = {'build_ext': build_ext,'build_scripts':build_scripts, 'install_scripts':install_scripts},
-      requires=['Cython (>=0.16)'],
+      install_requires=requires,
       zip_safe = False,
       ext_modules=EXTENTION)
 

src/obitaxonomy.py

@@ -202,8 +202,8 @@ if __name__ == '__main__':
     
     localdata=False
     
-    if options.write != '' :
+#     if options.write != '' :
-        options.write = open(options.write, 'w')
+#         options.write = open(options.write, 'w')
     
     for t in options.newtaxon:
         tx = t.split(':')

src/obitools/ecopcr/__init__.py

@@ -1,296 +1,69 @@
+from obitools import utils
+from obitools import NucSequence
+from obitools.utils import universalOpen, universalTell, fileSize, progressBar
+import struct
 import sys
 
-import time
-import re
-import shelve
 
-from threading import Lock
+class EcoPCRFile(utils.ColumnFile):
-from logging  import warning
+    def __init__(self,stream):
-import urllib2
+        utils.ColumnFile.__init__(self,
+                                  stream, '|', True, 
+                                  (str,int,int,
+                                   str,int,str,
+                                   int,str,int,
+                                   str,int,str,
+                                   str,str,int,float,
+                                   str,int,float,
+                                   int,
+                                   str,str), "#")
 
-from obitools.gzip import GzipFile
-from obitools.zipfile import ZipFile
-import os.path
-
-from _utils import FakeFile
-from _utils import progressBar
-
-try:
-    from collections import Counter
-except ImportError:
-    from obitools.collections import Counter
-
-
-class FileFormatError(Exception):
-    pass
-
-
-
-def universalOpen(file,*options):
-    '''
-    Open a file gziped or not.
-    
-    If file is a C{str} instance, file is
-    concidered as a file name. In this case 
-    the C{.gz} suffixe is tested to eventually
-    open it a a gziped file.
-    
-    If file is an other kind of object, it is assumed
-    that this object follow the C{file} interface 
-    and it is return as is.
-    
-    @param file: the file to open
-    @type file: C{str} or a file like object
-    
-    @return: an iterator on text lines.
-    '''
-    if isinstance(file,str):
-        try:
-            if urllib2.urlparse.urlparse(file)[0]=='':
-                rep = open(file,*options)
-            else:
-                rep  = urllib2.urlopen(file,timeout=15)
-                    
-            if file[-3:] == '.gz':
-                rep = GzipFile(fileobj=rep)
-            if file[-4:] == '.zip':
-                zip = ZipFile(file=rep)
-                data = zip.infolist()
-                assert len(data)==1,'Only zipped file containning a single file can be open'
-                name = data[0].filename
-                rep = zip.open(name)
-        except Exception as e:
-            print>>sys.stderr, e
-            sys.exit();
-    else:
-        rep = file
-    return rep
-
-def universalTell(file):
-    '''
-    Return the position in the file even if
-    it is a gziped one.
-    
-    @param file: the file to check
-    @type file: a C{file} like instance
-    
-    @return: position in the file
-    @rtype:  C{int}
-    '''
-    if isinstance(file, GzipFile):
-        file=file.myfileobj
-    return file.tell()
-
-def fileSize(file):
-    '''
-    Return the file size even if it is a 
-    gziped one.
-    
-    @param file: the file to check
-    @type file: a C{file} like instance
-    
-    @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)
-    return length
-
-
-def endLessIterator(endedlist):
-    for x in endedlist:
-        yield x
-    while(1):
-        yield endedlist[-1]
-    
-    
-def multiLineWrapper(lineiterator):
-    '''
-    Aggregator of strings.
-    
-    @param lineiterator: a stream of strings from an opened OBO file.
-    @type lineiterator: a stream of strings.
-    
-    @return: an aggregated stanza.
-    @rtype: an iterotor on str
-    
-    @note: The aggregator aggregates strings from an opened OBO file.
-    When the length of a string is < 2, the current stanza is over.
-    '''
-    
-    for line in lineiterator:
-        rep = [line]
-        while len(line)>=2 and line[-2]=='\\':
-            rep[-1]=rep[-1][0:-2]
-            try:
-                line = lineiterator.next()
-            except StopIteration:
-                raise FileFormatError
-            rep.append(line)
-        yield ''.join(rep)
-    
-    
-def skipWhiteLineIterator(lineiterator):
-    '''
-    Curator of stanza.
-    
-    @param lineiterator: a stream of strings from an opened OBO file.
-    @type lineiterator: a stream of strings.
-    
-    @return: a stream of strings without blank strings.
-    @rtype: a stream strings
-    
-    @note: The curator skip white lines of the current stanza.
-    '''
-    
-    for line in lineiterator:
-        cleanline = line.strip()
-        if cleanline:
-            yield line
-        else:
-            print 'skipped'
-    
-
-class ColumnFile(object):
-    
-    def __init__(self,stream,sep=None,strip=True,
-                 types=None,skip=None,head=None,
-                 extra=None,
-                 extraformat='([a-zA-Z]\w*) *= *([^;]+);'):
-        self._stream = universalOpen(stream)
-        self._delimiter=sep
-        self._strip=strip
-        self._extra=extra
-        self._extraformat = re.compile(extraformat)
-        
-        if types:
-            self._types=[x for x in types]
-            for i in xrange(len(self._types)):
-                if self._types[i] is bool:
-                    self._types[i]=ColumnFile.str2bool
-        else:
-            self._types=None
-        
-        self._skip = skip
-        if skip is not None:
-            self._lskip= len(skip)
-        else:
-            self._lskip= 0
-        self._head=head
-            
-    def str2bool(x):
-        return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
-                    
-    str2bool = staticmethod(str2bool)
-            
-        
-    def __iter__(self):
-        return self
 
     def next(self):
+        data = utils.ColumnFile.next(self)
+        seq = NucSequence(data[0],data[20],data[21])
+        seq['seq_length_ori']=data[1]
+        seq['taxid']=data[2]
+        seq['rank']=data[3]
+        seq['species']=data[4]
+        seq['species_name']=data[5]
+        seq['genus']=data[6]
+        seq['genus_name']=data[7]
+        seq['family']=data[8]
+        seq['family_name']=data[9]
+        seq['strand']=data[12]
+        seq['forward_match']=data[13]
+        seq['forward_error']=data[14]
+        seq['forward_tm']=data[15]
+        seq['reverse_match']=data[16]
+        seq['reverse_error']=data[17]
+        seq['reverse_tm']=data[18]
                  
-        def cast(txt,type):
-            try:
-                v = type(txt)
-            except:
-                v=None
-            return v
-        ligne = self._stream.next()
-        if self._skip is not None:
-            while ligne[0:self._lskip]==self._skip:
-                ligne = self._stream.next()
-        if self._extra is not None:
-            try:
-                (ligne,extra) = ligne.rsplit(self._extra,1)
-                extra = dict(self._extraformat.findall(extra))
-            except ValueError:
-                extra=None
-        else:
-            extra = None
-        data = ligne.split(self._delimiter)
-        if self._strip or self._types:
-            data = [x.strip() for x in data]
-        if self._types:
-            it = endLessIterator(self._types)
-            data = [cast(*x) for x in ((y,it.next()) for y in data)]
-        if self._head is not None:
-            data=dict(map(None, self._head,data))
-            if extra is not None:
-                data['__extra__']=extra
-        else:
-            if extra is not None:
-                data.append(extra)
-        return data
-    
-    def tell(self):
-        return universalTell(self._stream)
-
-                    
-class CachedDB(object):
-    
-    def __init__(self,cachefile,masterdb):
-        self._cache = shelve.open(cachefile,'c')
-        self._db = masterdb
-        self._lock=Lock()
-        
-    def _cacheSeq(self,seq):
-        self._lock.acquire()
-        self._cache[seq.id]=seq
-        self._lock.release()
         return seq
     
-    def __getitem__(self,ac):
-        if isinstance(ac,str):
-            self._lock.acquire()
-            if ac in self._cache:
-#                print >>sys.stderr,"Use cache for %s" % ac
-                data = self._cache[ac]
-                self._lock.release()
         
-            else:
+        
-                self._lock.release()
+class EcoPCRDBFile(object):
-                data = self._db[ac]
+    
-                self._cacheSeq(data)
+    def _ecoRecordIterator(self,file,noError=False):
-            return data
+        file = universalOpen(file,noError)
+        (recordCount,) = struct.unpack('> I',file.read(4))
+        self._recover=False
+    
+        if recordCount:
+            for i in xrange(recordCount):
+                (recordSize,)=struct.unpack('>I',file.read(4))
+                record = file.read(recordSize)
+                yield record
         else:
-            self._lock.acquire()
+            print >> sys.stderr,"\n\n  WARNING : EcoPCRDB reading set into recover data mode\n"
-            acs = [[x,self._cache.get(x,None)] for x in ac]
+            self._recover=True
-            self._lock.release()
+            ok=True
-            newacs = [ac for ac,cached in acs if cached is None]
+            while(ok):
-            if newacs:
+                try:
-                newseqs = self._db[newacs]
+                    (recordSize,)=struct.unpack('>I',file.read(4))
-            else:
+                    record = file.read(recordSize)
-                newseqs = iter([])
+                    yield record
-            for r in acs:
+                except:
-                if r[1] is None:
+                    ok=False
-                    r[1]=self._cacheSeq(newseqs.next())
-#                else:
-#                    print >>sys.stderr,"Use cache for %s" % r[0]
-            return (x[1] for x in acs)
                 
-        
-def moduleInDevelopment(name):
-    Warning('This module %s is under development : use it with caution' % name)
-    
-            
-def deprecatedScript(newscript):
-    current = sys.argv[0]
-    print >>sys.stderr,"        "   
-    print >>sys.stderr,"        "   
-    print >>sys.stderr,"        "   
-    print >>sys.stderr,"#########################################################"
-    print >>sys.stderr,"#                                                       #"
-    print >>sys.stderr,"    W A R N I N G :"
-    print >>sys.stderr,"        %s is a deprecated script                     " % os.path.split(current)[1]
-    print >>sys.stderr,"        it will disappear in the next obitools version" 
-    print >>sys.stderr,"        "   
-    print >>sys.stderr,"    The new corresponding command is %s    " % newscript   
-    print >>sys.stderr,"#                                                       #"
-    print >>sys.stderr,"#########################################################"
-    print >>sys.stderr,"        "   
-    print >>sys.stderr,"        "   
-    print >>sys.stderr,"        "   

src/obitools/ecopcr/options.py

@@ -70,10 +70,9 @@ def loadTaxonomyDatabase(options):
 
     if isinstance(options.taxonomy, Taxonomy):
         return options.taxonomy
-    #taxonomy = ecobarcodeDatabaseConnection(options)
+
     taxonomy = None
-    if (taxonomy is not None or 
+    if (options.taxonomy is not None or 
-        options.taxonomy is not None or 
         options.taxdump is not None):
         if options.taxdump is not None:
             taxonomy = TaxonomyDump(options.taxdump)

src/obitools/ecopcr/sequence.py

@@ -1,12 +1,14 @@
 from obitools import NucSequence
 from obitools.ecopcr import EcoPCRDBFile
 from obitools.ecopcr.taxonomy import EcoTaxonomyDB, ecoTaxonomyWriter
+from obitools.ecopcr.options  import loadTaxonomyDatabase
 from obitools.ecopcr.annotation import EcoPCRDBAnnotationWriter
 from obitools.utils import universalOpen
 from glob import glob
 import struct
 import gzip
 import sys
+import re
 
 
 class EcoPCRDBSequenceIterator(EcoPCRDBFile):
@@ -40,11 +42,11 @@ class EcoPCRDBSequenceIterator(EcoPCRDBFile):
         for record in self._ecoRecordIterator(file):
             lrecord = len(record)
             lnames  = lrecord - (4*4+20)
-            (taxid,seqid,deflength,seqlength,cptseqlength,string)=struct.unpack('> I 20s I I I %ds' % lnames, record)
+            (taxid,seqid,deflength,seqlength,cptseqlength,string)=struct.unpack('> I 20s I I I %ds' % lnames, record)  # @UnusedVariable
             seqid=seqid.strip('\x00')
             de = string[:deflength]
             seq = gzip.zlib.decompress(string[deflength:])
-            bioseq = NucSequence(seqid,seq,de,taxidx=taxid,taxid=self._taxonomy._taxonomy[taxid][0])
+            bioseq = NucSequence(seqid,seq,de,taxid=self._taxonomy._taxonomy[taxid][0])
             yield  bioseq
         
     def __iter__(self):
@@ -54,8 +56,26 @@ class EcoPCRDBSequenceIterator(EcoPCRDBFile):
                 
 class EcoPCRDBSequenceWriter(object):
     
-    def __init__(self,dbname,fileidx=1,taxonomy=None,ftid=None,type=None,definition=None,append=False):
+    def __init__(self,options,fileidx=None,ftid=None,type=None,definition=None,append=False):
-        self._taxonomy=taxonomy
+
+        # Take care of the taxonomy associated to the database
+        
+        self._taxonomy= loadTaxonomyDatabase(options)
+        dbname=options.ecopcroutput
+        
+        if (self._taxonomy is not None
+            and (not hasattr(options,'ecodb') or options.ecodb!=dbname)):
+            print >> sys.stderr,"Writing the taxonomy file...",
+            ecoTaxonomyWriter(dbname,self._taxonomy)
+            print >> sys.stderr,"Ok"
+            
+        # Identifiy the next sequence file numbre 
+        if fileidx is None:
+            p = re.compile(r'([0-9]{3})\.sdx')
+            fileidx = max(list(int(p.search(i).group(1)) 
+                               for i in glob('%s_[0-9][0-9][0-9].sdx' % dbname))+[0]
+                          ) +1
+        
         self._filename="%s_%03d.sdx" % (dbname,fileidx)
         if append:
             mode ='r+b'
@@ -73,11 +93,6 @@ class EcoPCRDBSequenceWriter(object):
             self._file = open(self._filename,mode)
             self._file.write(struct.pack('> I',self._sequenceCount))
                 
-        if self._taxonomy is not None:
-            print >> sys.stderr,"Writing the taxonomy file...",
-            ecoTaxonomyWriter(dbname,self._taxonomy)
-            print >> sys.stderr,"Ok"
-        
         if type is not None:
             assert ftid is not None,"You must specify an id attribute for features"
             self._annotation = EcoPCRDBAnnotationWriter(dbname, ftid, fileidx, type, definition)

src/obitools/ecopcr/taxonomy.py

@@ -329,10 +329,10 @@ class EcoTaxonomyDB(Taxonomy,EcoPCRDBFile):
             
         try :
             lt=0
-            for record in self._ecoRecordIterator(self._localTaxonFile):
+            for record in self._ecoRecordIterator(self._localTaxonFile,noError=True):
                 lrecord = len(record)
                 lnames  = lrecord - 16
-                (taxid,rankid,parentidx,nameLength,name)=struct.unpack('> I I I I %ds' % lnames, record)
+                (taxid,rankid,parentidx,nameLength,name)=struct.unpack('> I I I I %ds' % lnames, record)  # @UnusedVariable
                 lt+=1
                 yield  (taxid,rankid,parentidx,name,'local')
             print >> sys.stderr, " [INFO : Local taxon file found] : %d added taxa" % lt
@@ -344,7 +344,7 @@ class EcoTaxonomyDB(Taxonomy,EcoPCRDBFile):
             yield  record
     
     def __ecoAliasIterator(self):
-        for record in self._ecoRecordIterator(self._aliasFile):
+        for record in self._ecoRecordIterator(self._aliasFile,noError=True):
             (taxid,index) = struct.unpack('> I i',record)
             yield taxid,index
             
@@ -402,7 +402,7 @@ class EcoTaxonomyDB(Taxonomy,EcoPCRDBFile):
                 
         try :
             self._preferedName = [(x[0],'obi',x[2]) 
-                                  for x in self.__ecoNameIterator(self._preferedNamesFile)]
+                                  for x in self.__ecoNameIterator(self._preferedNamesFile,noError=True)]
             print >> sys.stderr, " [INFO : Preferred taxon name file found] : %d added taxa" % len(self._preferedName)
         except:
             print >> sys.stderr, " [INFO : Preferred taxon name file not found]"

src/obitools/format/_format.pyx

@@ -2,7 +2,7 @@
 
 import sys
 from obitools.fasta import formatFasta
-from obitools.ecopcr.sequence import EcoPCRDBSequenceWriter
+#from obitools.ecopcr.sequence import EcoPCRDBSequenceWriter
 
 cpdef printOutput(options,seq,output=sys.stdout):
     if options.output is not None:

src/obitools/format/options.py

@@ -18,7 +18,6 @@ from obitools.fasta import formatFasta, rawFastaIterator,\
 from obitools.fastq import formatFastq
 
 from obitools.ecopcr.sequence import EcoPCRDBSequenceWriter
-from obitools.ecopcr.options  import loadTaxonomyDatabase
 
 from cPickle import dump,load,UnpicklingError
 
@@ -34,7 +33,7 @@ from obitools.format.sequence import skipOnErrorIterator
 from obitools import BioSequence
 from obitools.utils import FakeFile
 
-
+from glob import glob
 
 
 def binarySequenceIterator(lineiterator):    
@@ -168,7 +167,7 @@ def addOutputFormatOption(optionManager):
 #                             help="Output sequences in sap fasta format "
 #                                  "(Sequence must have a taxid and a taxonomy has to be loaded)")
     
-    group.add_option('--ecopcrDB-output',
+    group.add_option('--ecopcrdb-output',
                              action="store", dest="ecopcroutput",
                              default=None,
                              help="Output sequences in ecopcr database format "
@@ -313,6 +312,10 @@ def sequenceWriterGenerator(options,output=sys.stdout):
                         self._format=formatSAPFastaGenerator(options)
                 elif options.outputFormater is not None:
                     self._format=options.outputFormater
+                    
+            if hasattr(seq,'_hasTaxid') and seq._hasTaxid:
+                seq.extractTaxon()
+
             s = self._format(seq,upper=self._upper)
             try:
                 self._file.write(s)
@@ -336,8 +339,7 @@ def sequenceWriterGenerator(options,output=sys.stdout):
            
                 
     if options.ecopcroutput is not None:
-        taxo = loadTaxonomyDatabase(options)
+        writer=EcoPCRDBSequenceWriter(options)
-        writer=EcoPCRDBSequenceWriter(options.ecopcroutput,taxonomy=taxo)
     elif options.output==dump:
         writer=BinaryWriter(options,output)
     else:

src/obitools/options/_options.pyx

@@ -6,7 +6,7 @@ from obitools.utils import universalOpen
 from obitools.utils import universalTell
 from obitools.utils import fileSize
 from obitools.ecopcr.sequence import EcoPCRDBSequenceIterator
-
+from glob import glob 
 from logging import debug
 import sys
 
@@ -69,23 +69,30 @@ def allEntryIterator(files,entryIterator,with_progress=False,histo_step=102):
     if files :
         for f in files:
             if (entryIterator != EcoPCRDBSequenceIterator) :
+                          
                 cfs.currentInputFileName=f
-                f = universalOpen(f)
+                try:
-                cfs.currentFile=f
+                    f = universalOpen(f,noError=True)
-                cfs.currentFileSize=fileSize(cfs.currentFile)
+                except Exception as e:    
-                debug(f)
+                    if glob('%s_[0-9][0-9][0-9].sdx' % f):
-            
+                        entryIterator=EcoPCRDBSequenceIterator
-                if with_progress:
+                    else:
-                    f=fileWithProgressBar(f,step=histo_step)
+                        print >>sys.stderr, e
-                    
+                        sys.exit();
-                if entryIterator is None:
-                    for line in f:
-                        yield line
                 else:
-                    for entry in entryIterator(f):
+                    cfs.currentFile=f
-                        yield entry
+                    cfs.currentFileSize=fileSize(cfs.currentFile)
-            else :
+                    debug(f)
-                yield EcoPCRDBSequenceIterator(f)
+                
+                    if with_progress:
+                        f=fileWithProgressBar(f,step=histo_step)           
+                    
+            if entryIterator is None:
+                for line in f:
+                    yield line
+            else:
+                for entry in entryIterator(f):
+                    yield entry
  
     else:
         if entryIterator is None:

src/obitools/utils/__init__.py

@@ -26,7 +26,7 @@ class FileFormatError(Exception):
 
 
 
-def universalOpen(file,*options):
+def universalOpen(file,noError=False):
     '''
     Open a file gziped or not.
     
@@ -47,7 +47,7 @@ def universalOpen(file,*options):
     if isinstance(file,str):
         try:
             if urllib2.urlparse.urlparse(file)[0]=='':
-                rep = open(file,*options)
+                rep = open(file)
             else:
                 rep  = urllib2.urlopen(file,timeout=15)
                     
@@ -60,8 +60,11 @@ def universalOpen(file,*options):
                 name = data[0].filename
                 rep = zip.open(name)
         except Exception as e:
-            print>>sys.stderr, e
+            if not noError:
-            sys.exit();
+                print >>sys.stderr, e
+                sys.exit();
+            else:
+                raise e
     else:
         rep = file
     return rep