Switch to the version 1.1.21

illuminapairedend

setup.py

@@ -19,7 +19,7 @@ from os import path
 
 
 PACKAGE = "OBITools"
-VERSION = "1.1.19"
+VERSION = "1.1.21"
 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/obitools/format/options.py

@@ -313,11 +313,11 @@ 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)
 

src/obitools/version.py

@@ -1,5 +1,5 @@
 major = 1
 minor = 1
-serial= '19'
+serial= '21'
 
 version = "%2d.%02d %s" % (major,minor,serial)