debian/README.source

@@ -4,16 +4,16 @@ which is 0.4.0.
 
 You could try this by running
 
-$ python tests/test_sortmerna.py
+$ python3 tests/test_sortmerna.py
 Traceback (most recent call last):
   File "tests/test_sortmerna.py", line 16, in <module>
     from skbio.parse.sequences import parse_fasta
 ImportError: No module named parse.sequences
 
 
-The module interface was changed inbetween python-skbio version
+The module interface was changed inbetween python3-skbio version
 0.2.3 and 0.4.0.
 
 As a consequence the test is not run.  If you might succeed in
-adapting the code please add the Build-Depends python-skbio and
-python-lockfile.
+adapting the code please add the Build-Depends python3-skbio and
+python3-lockfile.

debian/changelog

+sortmerna (2.1-4) unstable; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #945707
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Secure URI in copyright format
+  * Use secure URI in Homepage field.
+  * Set upstream metadata fields: Bug-Database, Bug-Submit (from
+    ./configure), Repository, Repository-Browse.
+
+ -- Andreas Tille <tille@debian.org>  Wed, 25 Dec 2019 21:25:41 +0100
+
 sortmerna (2.1-3) unstable; urgency=medium
 
   [ Steffen Moeller ]

debian/compat

-11

debian/control

@@ -4,18 +4,21 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12),
+#               python3 <!nocheck>,
+#               python3-skbio <!nocheck>,
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/sortmerna
 Vcs-Git: https://salsa.debian.org/med-team/sortmerna.git
-Homepage: http://bioinfo.lifl.fr/RNA/sortmerna/
+Homepage: https://bioinfo.lifl.fr/RNA/sortmerna/
 
 Package: sortmerna
 Architecture: any-amd64 any-i386 x32
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          sse2-support [any-i386]
-Recommends: python
+Recommends: python3,
+#            python3-skbio
 Description: tool for filtering, mapping and OTU-picking NGS reads
  SortMeRNA is a biological sequence analysis tool for filtering, mapping and
  OTU-picking NGS reads. The core algorithm is based on approximate seeds and

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: SortMeRNA
 Upstream-Contact: jenya.kopylov@gmail.com, laurent.noe@lifl.fr, helene.touzet@lifl.fr
 Source: https://github.com/biocore/sortmerna

debian/patches/2to3.patch

+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: htts://bugs.debian.org/945707
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 25 Dec 2019 17:25:58 +0100
+
+--- a/README.md
++++ b/README.md
+@@ -114,7 +114,7 @@ Tests
+ 
+ Usage tests can be run with the following command:
+ ```
+-python ./tests/test_sortmerna.py
++python3 ./tests/test_sortmerna.py
+ ```
+ Make sure the ```data``` folder is in the same directory as ```test_sortmerna.py```
+ 
+--- a/rRNA_databases/scripts/hmmer_clean.sh
++++ b/rRNA_databases/scripts/hmmer_clean.sh
+@@ -21,7 +21,7 @@ for db in "${!databases[@]}"
+ do
+     hmms=(${databases["$db"]//,/ })
+ 
+-    echo "source /home/evko1434/.bashrc; $hmmer -o $outdir/${db}_vs_${hmms[0]}.txt --noali --tblout $outdir/${db}_vs_${hmms[0]}_table.txt --acc -E 1e-5 --cpu 20 ${rootdir}/HMM3/${hmms[0]}.hmm $rootdir/${db}.fasta; $hmmer -o $outdir/${db}_vs_${hmms[1]}.txt --noali --tblout $outdir/${db}_vs_${hmms[1]}_table.txt --acc -E 1e-5 --cpu 20 ${rootdir}/HMM3/${hmms[1]}.hmm $rootdir/${db}.fasta; python $rootdir/remove_partial_seqs.py $outdir/${db}_vs_${hmms[0]}_table.txt $outdir/${db}_partial_${hmms[0]}_to_remove.txt; python $rootdir/remove_partial_seqs.py $outdir/${db}_vs_${hmms[1]}_table.txt $outdir/${db}_partial_${hmms[1]}_to_remove.txt; cat $outdir/${db}_partial_${hmms[0]}_to_remove.txt $outdir/${db}_partial_${hmms[1]}_to_remove.txt > $outdir/${db}_partial_seqs_to_remove.txt; filter_fasta.py -f $rootdir/${db}.fasta -s $outdir/${db}_partial_seqs_to_remove.txt -n -o $rootdir/${db}_clean.fasta; python $rootdir/edit_U_to_T_rna.py $rootdir/${db}_clean.fasta $rootdir/${db}_clean-T.fasta" | qsub $qsub_param -N ${db}_clean; sleep 2
++    echo "source /home/evko1434/.bashrc; $hmmer -o $outdir/${db}_vs_${hmms[0]}.txt --noali --tblout $outdir/${db}_vs_${hmms[0]}_table.txt --acc -E 1e-5 --cpu 20 ${rootdir}/HMM3/${hmms[0]}.hmm $rootdir/${db}.fasta; $hmmer -o $outdir/${db}_vs_${hmms[1]}.txt --noali --tblout $outdir/${db}_vs_${hmms[1]}_table.txt --acc -E 1e-5 --cpu 20 ${rootdir}/HMM3/${hmms[1]}.hmm $rootdir/${db}.fasta; python3 $rootdir/remove_partial_seqs.py $outdir/${db}_vs_${hmms[0]}_table.txt $outdir/${db}_partial_${hmms[0]}_to_remove.txt; python3 $rootdir/remove_partial_seqs.py $outdir/${db}_vs_${hmms[1]}_table.txt $outdir/${db}_partial_${hmms[1]}_to_remove.txt; cat $outdir/${db}_partial_${hmms[0]}_to_remove.txt $outdir/${db}_partial_${hmms[1]}_to_remove.txt > $outdir/${db}_partial_seqs_to_remove.txt; filter_fasta.py -f $rootdir/${db}.fasta -s $outdir/${db}_partial_seqs_to_remove.txt -n -o $rootdir/${db}_clean.fasta; python3 $rootdir/edit_U_to_T_rna.py $rootdir/${db}_clean.fasta $rootdir/${db}_clean-T.fasta" | qsub $qsub_param -N ${db}_clean; sleep 2
+ done
+ 
+ 
+--- a/tests/test_sortmerna.py
++++ b/tests/test_sortmerna.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """
+ Software tests for the SortMeRNA (development version)
+ ======================================================
+@@ -230,7 +230,7 @@ class SortmernaTests(TestCase):
+ 
+ 
+     def test_indexdb_default_param(self):
+-    	""" Test indexing a database using SortMeRNA
++        """ Test indexing a database using SortMeRNA
+         """
+         index_db = join(self.output_dir, "db_gg_13_8")
+         index_path = "%s,%s" % (self.db_gg_13_8, index_db)
+@@ -352,7 +352,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -432,7 +432,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -539,7 +539,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -666,7 +666,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -792,7 +792,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -912,7 +912,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -994,7 +994,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         # Correct number of clusters in OTU-map
+         with open(aligned_basename + ".log", 'U') as f_log:
+@@ -1059,7 +1059,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -1118,7 +1118,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -1177,7 +1177,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         f_log = open(aligned_basename + ".log", "U")
+         f_log_str = f_log.read()
+@@ -1251,7 +1251,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         sam_alignments_expected = [['GQ099317.1.1325_157_453_0:0:0_0:0:0_99/1',
+                                     '0',
+@@ -1335,7 +1335,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         expected_alignment = ["AB271211", "Unc49508", "93.4", "1412",
+                               "64", "30", "59", "1470", "2", "1429", "0",
+@@ -1388,7 +1388,7 @@ class SortmernaTests(TestCase):
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         expected_alignment = """Sequence ID: Unc49508 count=1; cluster_weight=4; cluster=Unc49508; cluster_score=1.000000; cluster_center=True; 
+ Query ID: AB271211 1487 residues
+@@ -1534,7 +1534,7 @@ Query:      1416    AGCTGGTCACGCCCGAAGTC
+ 
+         stdout, stderr = proc.communicate()
+         if stderr:
+-            print stderr
++            print(stderr)
+ 
+         expected_alignment = ["AB271211", "Unc49508", "93.4", "1412", "64", "30", "59", "1470", "2", "1429", "0", "2041"]
+ 

debian/patches/series

+2to3.patch

debian/rules

@@ -23,6 +23,12 @@ override_dh_auto_build:
 	mkdir -p tmp
 	cat debian/README_scripts.txt rRNA_databases/README.txt > tmp/README.txt
 
+# Uses old interface of skbio (see README.source)
+#override_dh_auto_test:
+#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+#	python3 ./tests/test_sortmerna.py
+#endif
+
 override_dh_auto_install:
 	#Skip this - do it manually
 	true

debian/upstream/metadata

@@ -10,10 +10,8 @@ Reference:
   Pages: 3211-3217
   DOI: 10.1093/bioinformatics/bts611
   PMID: 23071270
-  URL: "http://bioinformatics.oxfordjournals.org/content/\
-    28/24/3211"
-  eprint: "http://bioinformatics.oxfordjournals.org/content/\
-    28/24/3211.full.pdf+html"
+  URL: http://bioinformatics.oxfordjournals.org/content/28/24/3211
+  eprint: http://bioinformatics.oxfordjournals.org/content/28/24/3211.full.pdf+html
 Registry:
 - Name: OMICtools
   Entry: OMICS_02619
@@ -23,3 +21,7 @@ Registry:
   Entry: sortmerna
 - Name: SciCrunch
   Entry: SCR_014402
+Bug-Database: https://github.com/biocore/sortmerna/issues
+Bug-Submit: jenya DT kopylov AT gmail DT fr
+Repository: https://github.com/biocore/sortmerna.git
+Repository-Browse: https://github.com/biocore/sortmerna