Try to move packaging to Python3

obitools (1.2.13+dfsg-3) UNRELEASED; urgency=medium

  * Use 2to3 to port from Python2 to Python3

 -- Andreas Tille <tille@debian.org>  Sun, 12 Jan 2020 15:05:34 +0100

obitools (1.2.13+dfsg-2) unstable; urgency=medium

  * Apply patch by Olivier Sallou to work around bug at cleanup

Priority: optional

Build-Depends: debhelper-compat (= 12),

               dh-python,

               python-dev,

               python3-dev,

               python3-sphinx,

               cython,

               ipython,

               python-wheel,

               python-virtualenv

               cython3,

               ipython3,

               python3-wheel,

               python3-virtualenv

Standards-Version: 4.4.1

Vcs-Browser: https://salsa.debian.org/med-team/obitools

Vcs-Git: https://salsa.debian.org/med-team/obitools.git

Package: obitools

Architecture: amd64

Depends: ${misc:Depends},

         ${python:Depends},

         ${python3:Depends},

         ${shlibs:Depends},

         ${sphinxdoc:Depends},

         libjs-sphinxdoc

 #

--- a/src/ali2consensus.py

+++ b/src/ali2consensus.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 30 sept. 2011

@@ -63,7 +63,7 @@ if __name__=='__main__':

     iupacDNA['B'] = ('C', 'G', 'T')

     iupacDNA['N'] = ('A', 'C', 'G', 'T')

         sumCounts = 0

--- a/src/ecodbtaxstat.py

+++ b/src/ecodbtaxstat.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`ecodbtaxstat`: gives taxonomic rank frequency of a given ``ecopcr`` database   

 =====================================================================================

@@ -65,12 +65,12 @@ if __name__=='__main__':

             i+=1

             stats[t]=stats.get(t,0)+1

\ No newline at end of file

--- a/src/ecotag.py

+++ b/src/ecotag.py

@@ -1,4 +1,4 @@

-#!/usr/local/OBITools-1.1.22/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`ecotag`: assigns sequences to taxa

 ===========================================

@@ -320,7 +320,7 @@ if __name__=='__main__':

     taxonomy = loadTaxonomyDatabase(options)

     writer = sequenceWriterGenerator(options)

--- a/src/ecotaxspecificity.py

+++ b/src/ecotaxspecificity.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`ecotaxspecificity`: Evaluates barcode resolution

 =========================================================

@@ -112,7 +112,7 @@ if __name__=='__main__':

     digit = int(math.ceil(math.log10(ldb)))

     aligncount = ldb*(ldb+1)/2

      #   print "Lost Sequences:"

--- a/src/ecotaxstat.py

+++ b/src/ecotaxstat.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`ecotaxstat` : getting the coverage of an ecoPCR output compared to the original ecoPCR database

 ========================================================================================================

@@ -24,6 +24,7 @@ from obitools.options import getOptionMa

 from obitools.ecopcr.options import loadTaxonomyDatabase

--- a/src/extractreads.py

+++ b/src/extractreads.py

@@ -81,7 +81,7 @@ def cutQuality(s):

@@ -82,7 +82,7 @@ def cutQuality(s):

     def cumsum0(x):

         if x[0] < 0: x[0]=0

             x[i]+=x[i-1]

             if x[i]<0: x[i]=0

         return x

@@ -114,8 +114,8 @@ def cutQuality(s):

@@ -115,8 +115,8 @@ def cutQuality(s):

 def cutDirectReverse(entries):

     first = []

     lens = [len(x) for x in first]

     clen = {}

@@ -137,7 +137,7 @@ def cutDirectReverse(entries):

@@ -138,7 +138,7 @@ def cutDirectReverse(entries):

 def seqPairs(direct,reverse):

     for d in direct:

         yield(cutQuality(d),cutQuality(r))

@@ -151,7 +151,7 @@ def seq2words(seqs,options):

@@ -152,7 +152,7 @@ def seq2words(seqs,options):

         ls = len(s) - options.length + 1

             w =minword(s[wp:wp+options.length])

             if len(w)==options.length:

                 nw.add(w)              

@@ -186,23 +186,23 @@ if __name__ == '__main__':

@@ -187,23 +187,23 @@ if __name__ == '__main__':

     writer = sequenceWriterGenerator(options)

     if options.rdump is None:

     while len(wordlist)>0:

         w = wordlist.pop()

@@ -224,17 +224,17 @@ if __name__ == '__main__':

@@ -225,17 +225,17 @@ if __name__ == '__main__':

         seqpair+=i

         if i:

--- a/src/extractreads2.py

+++ b/src/extractreads2.py

@@ -47,8 +47,8 @@ def addWindowsOptions(optionManager):

@@ -48,8 +48,8 @@ def addWindowsOptions(optionManager):

 def cutDirectReverse(entries):

     first = []

     lens = [len(x) for x in first]

     clen = {}

@@ -70,7 +70,7 @@ def cutDirectReverse(entries):

@@ -71,7 +71,7 @@ def cutDirectReverse(entries):

 def seqPairs(direct,reverse):

     for d in direct:

         yield(d,r)

 if __name__ == '__main__':

@@ -99,7 +99,7 @@ if __name__ == '__main__':

@@ -100,7 +100,7 @@ if __name__ == '__main__':

             ft = ft + ft[0:options.length]

             rt = rt + rt[0:options.length]

                 words.enter(w)

--- a/src/illuminapairedend.py

+++ b/src/illuminapairedend.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`illuminapairedend`: aligns paired-end Illumina reads

 =============================================================

@@ -52,7 +52,7 @@ from obitools.format.options import addO

     sequenceWriterGenerator

         writer(consensus)

--- a/src/ngsfilter.py

+++ b/src/ngsfilter.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`ngsfilter` : Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers

 ===================================================================================================================

@@ -46,6 +46,7 @@ from obitools.options import getOptionMa

 from obitools.utils import ColumnFile

 from obitools.align import FreeEndGapFullMatch

             message = 'No reverse primer match'

--- a/src/obiaddtaxids.py

+++ b/src/obiaddtaxids.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obiaddtaxids`: adds *taxids* to sequence records using an ecopcr database

 ==================================================================================

@@ -369,7 +369,7 @@ if __name__=='__main__':

                 try:

                     taxid = getTaxid(tax, species_name, restricting_ancestor)

                 if options.unidentified is not None and not genusFound :

-                    print>>options.unidentified,formatFasta(s)

+                    print(formatFasta(s), file=options.unidentified)

--- a/src/obiannotate.py

+++ b/src/obiannotate.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obiannotate`: adds/edits sequence record annotations

--- a/src/obiclean.py

+++ b/src/obiclean.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obiclean`: tags a set of sequences for PCR/sequencing errors identification 

@@ -165,7 +165,7 @@ if __name__ == '__main__':

     digit = int(math.ceil(math.log10(ldb)))

     aligncount = ldb*(ldb+1)/2

--- a/src/obicomplement.py

+++ b/src/obicomplement.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 """

 :py:mod:`obicomplement`: reverse-complements sequences

 ======================================================

--- a/src/obiconvert.py

+++ b/src/obiconvert.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obiconvert`: converts sequence files to different output formats

 =========================================================================

@@ -47,7 +47,7 @@ if __name__ == '__main__':

             try:

                 writer(entry)

--- a/src/obicount.py

+++ b/src/obicount.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obicount`: counts the number of sequence records 

 =========================================================

@@ -51,9 +51,9 @@ if __name__ == '__main__':

             count2+=1

\ No newline at end of file

--- a/src/obicut.py

+++ b/src/obicut.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obicut`: trims sequences

 =================================

@@ -48,6 +48,6 @@ if __name__=='__main__':  # @UndefinedVa

     writer = sequenceWriterGenerator(options)

\ No newline at end of file

--- a/src/obidistribute.py

+++ b/src/obidistribute.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obidistribute`: Distributes sequence records over several sequence records files 

 =========================================================================================

@@ -26,6 +26,7 @@ from obitools.format.options import addI

 import math

 from obitools.fasta import formatFasta

         out[i](seq)

--- a/src/obiextract.py

+++ b/src/obiextract.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obiextract`: extract samples from a dataset 

 ====================================================

@@ -56,7 +56,7 @@ def selectSamples(entry,key,samples):

         entry['count']=s 

         entry[key]=newsamples

     else:

         entry=None

--- a/src/obigrep.py

+++ b/src/obigrep.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obigrep`: filters sequence file 

 ========================================

--- a/src/obihead.py

+++ b/src/obihead.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obihead`: extracts the first sequence records

 ======================================================

@@ -50,7 +50,7 @@ if __name__ == '__main__':

             writer(s)

             i+=1

--- a/src/obijoinpairedend.py

+++ b/src/obijoinpairedend.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obijoinpairedend`: Joins paired-end reads

 ==================================================

@@ -54,8 +54,8 @@ def addPairEndOptions(optionManager):

 def cutDirectReverse(entries):

     first = []

--- a/src/obipr2.py

+++ b/src/obipr2.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obipr2`: converts silva database into an ecoPCR database

 =================================================================

@@ -35,7 +35,7 @@ from obitools.fasta import fastaIterator

 import sys

 from obitools.utils import universalOpen, ColumnFile

\ No newline at end of file

--- a/src/obisample.py

+++ b/src/obisample.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obisample`: randomly resamples sequence records

 ========================================================

@@ -39,7 +39,7 @@ def addSampleOptions(optionManager):

                             )

--- a/src/obiselect.py

+++ b/src/obiselect.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 """

 :py:mod:`obiselect` : selects representative sequence records

 =============================================================

@@ -18,6 +18,7 @@ from obitools.utils import progressBar

 import math

 import sys

+    print(file=sys.stderr)

--- a/src/obisilva.py

+++ b/src/obisilva.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obisilva`: converts silva database into an ecoPCR database

 ===================================================================

@@ -24,7 +24,7 @@ from obitools.fasta import fastaIterator

 import sys

 from obitools.utils import universalOpen, ColumnFile

     ecoTaxonomyWriter(options.ecopcroutput,options.taxonomy,onlyLocal=True)

--- a/src/obisort.py

+++ b/src/obisort.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obisort`: Sorts sequence records according to the value of a given attribute 

 =====================================================================================

--- a/src/obisplit.py

+++ b/src/obisplit.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obisplit`: Splits a sequence file in a set of subfiles

 ===============================================================

@@ -30,6 +30,7 @@ from obitools.options import getOptionMa

 from obitools.format.options import addInOutputOption

 from obitools.fasta import formatFasta

--- a/src/obistat.py

+++ b/src/obistat.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obistat`: computes basic statistics for attribute values 

 =================================================================

@@ -24,6 +24,7 @@ from obitools.options import getOptionMa

 from obitools.format.options import addInputFormatOption

 from obitools.ecopcr.options import addTaxonomyDBOptions, loadTaxonomyDatabase

 ================================================

--- a/src/obitab.py

+++ b/src/obitab.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obitab`: converts a sequence file to a tabular file

 ============================================================

@@ -75,7 +75,7 @@ if __name__=='__main__':

     db = []

     for seq in entries: 

--- a/src/obitail.py

+++ b/src/obitail.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obitail`: extracts the last sequence records

 =====================================================

--- a/src/obitaxonomy.py

+++ b/src/obitaxonomy.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obitaxonomy`: manages taxonomic databases

 ==================================================

@@ -87,9 +87,9 @@ def addTaxonFromFile(name, rank, parent,

     parent= options.taxonomy._taxonomy[taxon[2]]

             definition,info = parseFastaDescription(ds)

--- a/src/obitools/barcodecoverage/calcBc.py

+++ b/src/obitools/barcodecoverage/calcBc.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 24 nov. 2011

@@ -46,7 +46,7 @@ def main(amplifiedSeqs, seqsFromDB, kept

     BcValues = {}

         if g in amplifiedtaxabygroup :

--- a/src/obitools/barcodecoverage/drawBcTree.py

+++ b/src/obitools/barcodecoverage/drawBcTree.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 25 nov. 2011

@@ -100,9 +100,9 @@ def label(node):

+                      cartoon=cartoonRankGenerator('family')))

                       #collapse=collapseBcGenerator(70))

--- a/src/obitools/barcodecoverage/findErrors.py

+++ b/src/obitools/barcodecoverage/findErrors.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 24 nov. 2011

--- a/src/obitools/barcodecoverage/readFiles.py

+++ b/src/obitools/barcodecoverage/readFiles.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 23 nov. 2011

--- a/src/obitools/barcodecoverage/writeBcTree.py

+++ b/src/obitools/barcodecoverage/writeBcTree.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 25 nov. 2011

@@ -32,7 +32,7 @@ def main(BcValues,errors,tax) :

     for taxon in BcValues:

                              data[5],

--- a/src/obitools/solexaPairEnd.py

+++ b/src/obitools/solexaPairEnd.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 Created on 30 dec. 2009

@@ -26,8 +26,8 @@ def addSolexaPairEndOptions(optionManage

 def cutDirectReverse(entries):

     first = []

         def addToZip(zf, path, zippath):

--- a/src/obiuniq.py

+++ b/src/obiuniq.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`obiuniq`: groups and dereplicates sequences  

 ====================================================

@@ -104,4 +104,4 @@ if __name__=='__main__':

     uniqSeq=usm(entries,taxonomy,options.merge,options.mergeids,options.categories)

+        print(formatFasta(seq)) 

--- a/src/oligotag.py

+++ b/src/oligotag.py

@@ -1,4 +1,4 @@

-#!/usr/local/bin/python

+#!/usr/bin/python3

 '''

 :py:mod:`oligotag`: Designs a set of oligonucleotides with specified properties

 ===============================================================================

@@ -47,13 +47,13 @@ def addOligoTagOptions(optionManager):

 def edgeIterator(words,distmin=1,error=None):

     words=[x for x in words]

+        print("-------------------------------------------", file=sys.stderr)

+        print(file=sys.stderr)

--- a/src/obitools/options/_bioseqfilter.pyx

+++ b/src/obitools/options/_bioseqfilter.pyx

@@ -1,7 +1,7 @@

 # cython: profile=True

 from obitools.options.taxonomyfilter import taxonomyFilterGenerator

-

+from functools import reduce

 def filterGenerator(options):

     taxfilter = taxonomyFilterGenerator(options)

use_debian_libs

fix_path_interpreter

# 2to3.patch

2to3.patch