Switch to version 1.1.22

than one category

setup.py

@@ -19,7 +19,7 @@ from os import path
 
 
 PACKAGE = "OBITools"
-VERSION = "1.1.19"
+VERSION = "1.1.22"
 AUTHOR  = 'Eric Coissac'
 EMAIL   = 'eric@coissac.eu'
 URL     = 'metabarcoding.org/obitools'

src/ecotag.py

@@ -352,7 +352,7 @@ if __name__=='__main__':
 
     search = lcsIteratorSelf(entries,db,options)
                      
-    print >>sys.stderr,'\nCache size : %d\n'
+    print >>sys.stderr,'\nCache size : %d\n' % __CACHE_SIZE__
 
                     
     for seq,best,match in search:
@@ -442,7 +442,7 @@ if __name__=='__main__':
                         
         
         writer(seq)        
-    print >>sys.stderr,'\n%5.3f% of the alignments was cached' % (__INCache__/(__INCache__+__OUTCache__)*100)         
+    print >>sys.stderr,'\n%5.3f%% of the alignments was cached' % (__INCache__/(__INCache__+__OUTCache__)*100)         
                 
                     
                 

src/illuminapairedend.py

@@ -48,13 +48,14 @@ from obitools.options import getOptionManager, allEntryIterator
 from obitools.align import QSolexaReverseAssemble
 from obitools.align import QSolexaRightReverseAssemble
 from obitools.tools._solexapairend import buildConsensus
-from obitools.format.options import addInputFormatOption,addOutputFormatOption,\
+from obitools.format.options import addOutputFormatOption,\
     sequenceWriterGenerator
 
 from itertools import chain
 import cPickle
 import math
-from obitools.fastq._fastq import fastqIterator
+from obitools.fastq._fastq import fastqIterator  # @UnresolvedImport
+
 
 def addSolexaPairEndOptions(optionManager):
     optionManager.add_option('-r','--reverse-reads',
@@ -90,14 +91,6 @@ def addSolexaPairEndOptions(optionManager):
                              const='illumina',
                              help="input file is in fastq nucleic format produced by old solexa sequencer")
 
-#    optionManager.add_option('--proba',
-#                             action="store", dest="proba",
-#                             metavar="<FILENAME>",
-#                             type="str",
-#                             default=None,
-#                             help="null ditribution data file")
-    
-
     optionManager.add_option('--score-min',
                              action="store", dest="smin",
                              metavar="#.###",
@@ -105,13 +98,6 @@ def addSolexaPairEndOptions(optionManager):
                              default=None,
                              help="minimum score for keeping aligment")
 
-#    optionManager.add_option('--pvalue',
-#                             action="store", dest="pvalue",
-#                             metavar="#.###",
-#                             type="float",
-#                             default=None,
-#                             help="maximum pvalue for keeping aligment")
-    
 
 
 def cutDirectReverse(entries):
@@ -222,6 +208,8 @@ if __name__ == '__main__':
     
     #WARNING TO REMOVE : DIRTY PATCH !
     options.proba = None
+    options.skip  = None
+    options.only  = None
 
 
     options.sminL = None

src/obiselect.py

@@ -179,7 +179,7 @@ if __name__ == '__main__':
     i=0
     for c in classes:
         i+=1
-        progressBar(i,lclasses,False,"%15s" % c)
+        progressBar(i,lclasses,False,"%15s" % ("/".join(map(str,c)),))
         seqs = classes[c]
         sortclass(seqs, options)
         if len(c)==1:

src/obitools/format/options.py

@@ -33,10 +33,6 @@ from obitools.format.sequence import skipOnErrorIterator, skipfirst, only
 from obitools import BioSequence
 from obitools.utils import FakeFile
 
-from glob import glob
-from test.test_compiler import Toto
-
-
 def binarySequenceIterator(lineiterator):    
             
     f = FakeFile(lineiterator)
@@ -263,9 +259,9 @@ def autoEntriesIterator(options):
             raise AssertionError,'file is not in fasta, fasta, embl, genbank or ecoPCR format'
         
         if reader==binarySequenceIterator:
-            input = binarySequenceIterator(lineiterator)
+            input = binarySequenceIterator(lineiterator)  # @ReservedAssignment
         else:
-            input = reader(chain([first],lineiterator))
+            input = reader(chain([first],lineiterator))  # @ReservedAssignment
     
         return input
                 
@@ -313,11 +309,11 @@ def autoEntriesIterator(options):
     if options.skiperror:
         reader = skipOnErrorIterator(reader)
         
-    if options.skip is not None:
+    if hasattr(options, 'skip') and options.skip is not None:
         print >>sys.stderr,"Skipping %d sequences" % options.skip
         reader = skipfirst(reader,options.skip)
         
-    if options.only is not None:
+    if hasattr(options, 'only') and options.only is not None:
         print >>sys.stderr,"Analysing only %d sequences" % options.only
         reader = only(reader,options.only)
 
@@ -325,7 +321,7 @@ def autoEntriesIterator(options):
 
 def sequenceWriterGenerator(options,output=sys.stdout):
     class SequenceWriter:
-        def __init__(self,options,file=sys.stdout):
+        def __init__(self,options,file=sys.stdout):  # @ReservedAssignment
             self._format=None
             self._file=file
             self._upper=options.uppercase
@@ -350,7 +346,7 @@ def sequenceWriterGenerator(options,output=sys.stdout):
                 sys.exit(0)
                 
     class BinaryWriter:
-        def __init__(self,options,file=sys.stdout):
+        def __init__(self,options,file=sys.stdout):  # @ReservedAssignment
             self._file=file
             self._file.write("#!Pickle\n")
         def put(self,seq):

src/obitools/version.py

@@ -1,5 +1,5 @@
 major = 1
 minor = 1
-serial= '19'
+serial= '22'
 
 version = "%2d.%02d %s" % (major,minor,serial)