debian/README.Debian

+gasic for Debian
+================
+
+The run_mappers.py script contained code relying on SeQan 1.  This was replaced
+by SeQan 2 in Debian which does not contain the executable mason any more. The
+original command:
+
+   mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o <out> <ref>
+
+was replaced by 
+
+   mason_simulator illumina --illumina-read-length 10000 -o <out> <ref>
+
+It is not sure whether this provides comparable results.  If you have a better
+suggestion please write a bug report via
+
+   reportbug gasic
+
+ -- Andreas Tille <tille@debian.org>  Tue, 08 Oct 2019 15:01:07 +0200

debian/changelog

+gasic (0.0.r19-5) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #936582
+  * In run_mappers.py the executable mason from seqan-apps version 1.x
+    was called.  This is not available any more in seqan-apps 2.x and
+    thus it was replaced by mason_simulator.  Hope that's OK.
+
+ -- Andreas Tille <tille@debian.org>  Tue, 08 Oct 2019 15:01:07 +0200
+
 gasic (0.0.r19-4) unstable; urgency=medium
 
   * debhelper 11

debian/control

@@ -6,7 +6,8 @@ Uploaders: Andreas Tille <tille@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
-               python-all-dev,
+               dh-python,
+               python3,
                bowtie2
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/gasic
@@ -16,12 +17,12 @@ Homepage: http://sourceforge.net/projects/gasic/
 Package: gasic
 Architecture: any
 Depends: ${misc:Depends},
-         ${python:Depends},
-         python-scipy,
-         python-numpy,
-         python-biopython,
-         python-pysam,
-         python-matplotlib,
+         ${python3:Depends},
+         python3-scipy,
+         python3-numpy,
+         python3-biopython,
+         python3-pysam,
+         python3-matplotlib,
          bowtie,
          bowtie2,
          bwa,

debian/patches/2to3.patch

+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936582
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 08 Oct 2019 15:01:07 +0200
+
+--- a/core/gasic.py
++++ b/core/gasic.py
+@@ -46,7 +46,7 @@ def similarity_correction(sim, reads, N)
+     A = sim
+     r = reads.astype(np.float) / N
+ 
+-    rng = range(len(reads))
++    rng = list(range(len(reads)))
+     
+     # Now solve the optimization problem: min_c |Ac-r|^2 s.t. c_i >= 0 and 1-sum(c_i) >= 0
+     # construct objective function
+@@ -179,7 +179,7 @@ def bootstrap(reads, smat_raw, B, test_c
+ 
+         # check if the calculated abundance is below the test abundance
+         fails[b,:] = corr[b,:] < test_c
+-    print
++    print()
+     p_values = np.mean(fails, axis=0)
+     abundances = np.mean(corr, axis=0)
+     variances = np.var(corr, axis=0)
+--- a/core/tools.py
++++ b/core/tools.py
+@@ -54,19 +54,19 @@ def read_names(filename):
+ 
+ def run_bowtie2(index, reads, out, param=""):
+     command = "bowtie2 -U {reads} -x {index} -S {samfile} {param} --local -M 0 ".format(reads=reads, index=index, samfile=out, param=param)
+-    print "Executing:",command
++    print("Executing:",command)
+     os.system(command)
+     return 1
+ 
+ def run_bowtie(index, reads, out, param=""):
+     command = "bowtie -S -p 2 -q -3 30 -v 2 {param} {index} {reads} > {samfile}".format(index=index, reads=reads, samfile=out, param=param)
+-    print "Executing:",command
++    print("Executing:",command)
+     os.system(command)
+     return 1
+ 
+ def run_bwa(index, reads, out, param=""):
+     command = "bwa aln {param} {index} {reads} > /tmp/res.sai".format(index=index, reads=reads, param=param)
+-    print "Executing:",command
++    print("Executing:",command)
+     os.system(command)
+     # convert the bwa output to SAM and remove temporary file
+     command_sam = "bwa samse %s /tmp/res.sai %s > %s && rm /tmp/res.sai"%(index,reads,out)
+@@ -75,7 +75,7 @@ def run_bwa(index, reads, out, param="")
+ 
+ def run_bwasw(index, reads, out, param=""):
+     command = "bwa bwasw {param} {index} {reads} > {samfile}".format(index=index, reads=reads, samfile=out, param=param)
+-    print "Executing:",command
++    print("Executing:",command)
+     os.system(command)
+     return 1
+ 
+@@ -116,7 +116,7 @@ How to add your custom mapper
+ 
+ def run_mason_illumina(ref, out):
+     command = "mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o %s %s"%(out,ref)
+-    print "Executing:",command
++    print("Executing:",command)
+     os.system(command)
+     # remove the needless SAM file
+     command = "rm %s.sam"%out
+@@ -125,7 +125,7 @@ def run_mason_illumina(ref, out):
+ 
+ def run_dwgsim(ref, out):
+     command = "dwgsim -c 2 -1 80 -2 0 -r 0 -y 0 -e 0.002 -N 100000 -f TACG %s %s"%(ref, out)
+-    print "Executing:",command
++    print("Executing:",command)
+     os.system(command)
+     # remove all additional files and rename reads file
+     command = "mv {out}.bfast.fastq {out} && rm {out}.bwa.read1.fastq && rm {out}.bwa.read2.fastq && rm {out}.mutations.txt".format(out=out)
+--- a/correct_abundances.py
++++ b/correct_abundances.py
+@@ -55,10 +55,10 @@ def similarity_correction(names, smat_ra
+     p:                 p-value for the confidence, that the true abundance is above some threshold
+     """
+ 
+-    print "\n--- GASiC correction\n"
++    print("\n--- GASiC correction\n")
+     # find out the number of reads
+     total = len( [1 for read in pysam.Samfile(sam_pattern%(names[0]), "r")] )
+-    print "    found %i reads"%total
++    print("    found %i reads"%total)
+ 
+     # initialize some arrays
+     #   mapping information; mapped[i,j]=1 if read j was successfully mapped to i.
+@@ -67,7 +67,7 @@ def similarity_correction(names, smat_ra
+     #   total number of successfully mapped reads per reference
+     num_reads = np.zeros( (len(names),) )
+ 
+-    print "\n--- Analyzing SAM files\n"
++    print("\n--- Analyzing SAM files\n")
+     # analyze the SAM files
+     for n_ind,nm in enumerate(names):
+         msg = "    SAM file %i of %i"%(n_ind+1,len(names))
+@@ -82,12 +82,12 @@ def similarity_correction(names, smat_ra
+         mapped[n_ind,:] = np.array([int(not rd.is_unmapped) for rd in sf])
+         num_reads[n_ind] = sum(mapped[n_ind,:])
+ 
+-    print "\n\n--- Bootstrapping abundances\n"
++    print("\n\n--- Bootstrapping abundances\n")
+     # run similarity correction step
+     p,corr,var = gasic.bootstrap(mapped, smat_raw, bootstrap_samples)
+     err = np.sqrt(var)
+ 
+-    print "\nDone estimating abundances\n"
++    print("\nDone estimating abundances\n")
+     return total,num_reads,corr,err,p
+     
+ 
+@@ -170,7 +170,7 @@ See the provided LICENSE file or source
+             out = "{name}\t{mapped}\t{corr}\t{error}\t{pval}\n"
+             ofile.write(out.format(name=nm,mapped=num_reads[n_ind],corr=corr[n_ind]*total,error=err[n_ind]*total,pval=p[n_ind]))
+         ofile.close()
+-        print "--- wrote results to", opt.out
++        print("--- wrote results to", opt.out)
+ 
+     else:
+         parser.print_help()
+--- a/create_matrix.py
++++ b/create_matrix.py
+@@ -63,14 +63,14 @@ def similarity_matrix_raw(names, ref_pat
+         os.makedirs(temp_dir)
+     
+     n_seq = len(names)
+-    rng = range(n_seq)
++    rng = list(range(n_seq))
+ 
+     # construct arrays with real file names from pattern
+     ref_files = [ ref_pattern%nm for nm in names ] # filenames of reference sequences
+     index_files = [ index_pattern%nm for nm in names ]   # filenames of mapper index files
+     sim_files = [ temp_dir+'/'+nm+'.fastq' for nm in names ] # filenames of simulated read files
+     
+-    print "\n--- Simulating reads for each reference genome with %s\n"%simulator
++    print("\n--- Simulating reads for each reference genome with %s\n"%simulator)
+     # generate reads for every reference genome
+     for i in rng:
+         tools.run_simulator[simulator](ref_files[i], sim_files[i])
+@@ -80,14 +80,14 @@ def similarity_matrix_raw(names, ref_pat
+     # and are stored in fastq format
+     num_reads = len( [ True for i in SeqIO.parse(sim_files[0],'fastq') ] )
+ 
+-    print "\n--- Mapping simulated reads to reference genomes with %s\n"%mapper
++    print("\n--- Mapping simulated reads to reference genomes with %s\n"%mapper)
+     # map the reads of every reference to all references
+     for i in rng:
+         for j in rng:
+             samfile = temp_dir+'/'+names[i]+'-'+names[j]+'.sam'
+             tools.run_mapper[mapper](index_files[j], sim_files[i], samfile)
+ 
+-    print "\n--- Parsing SAM files\n"
++    print("\n--- Parsing SAM files\n")
+     # parse SAM files
+     mapped_reads = np.zeros((n_seq,n_seq, num_reads))
+     for i in rng:
+@@ -102,7 +102,7 @@ def similarity_matrix_raw(names, ref_pat
+             samhandle = pysam.Samfile(samfile, "r")
+             mapped_reads[i,j,:] = np.array( [int(not read.is_unmapped) for read in samhandle] )
+     
+-    print "\n\nMatrix creation done\n"
++    print("\n\nMatrix creation done\n")
+     
+     return mapped_reads
+ 
+@@ -152,7 +152,7 @@ See the provided LICENSE file or source
+ 
+         # save the similarity matrix
+         np.save(opt.out, smat)
+-        print "Wrote similarity matrix to",opt.out
++        print("Wrote similarity matrix to",opt.out)
+     else:
+         parser.print_help()
+         sys.exit(1)
+--- a/run_mappers.py
++++ b/run_mappers.py
+@@ -76,9 +76,9 @@ READS:  File containing the reads to be
+     
+         for i in range(len(names)):
+             msg = "--- mapping reads with %s to %s"%(options.mapper, ref[i])
+-            print msg
++            print(msg)
+             tools.run_mapper[options.mapper](ref[i], reads, out[i])
+-        print "\nMapping done.\n"
++        print("\nMapping done.\n")
+     else:
+         parser.print_help()
+         sys.exit(1)

debian/patches/series

+2to3.patch
 use_seqan_mason.patch
 fix_example_indentation.patch

debian/patches/use_seqan_mason.patch

@@ -4,14 +4,21 @@ Description: since there is a name conflict with mason and the Debian package
   mason is something else than the seqan tool, the code needs to be patched
   to find /usr/lib/seqan/bin/mason
 
---- gasic.orig/core/tools.py
-+++ gasic/core/tools.py
-@@ -115,7 +115,7 @@
+--- a/core/tools.py
++++ b/core/tools.py
+@@ -115,7 +115,14 @@ How to add your custom mapper
  # to create a seperate caller function for every scenario.
  
  def run_mason_illumina(ref, out):
 -    command = "mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o %s %s"%(out,ref)
-+    command = "/usr/lib/seqan/bin/mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o %s %s"%(out,ref)
-     print "Executing:",command
++    print("""Original command with mason from SeQan 1 was
++    mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o %s %s
++Please verify that the following call of mason_simulator fits your needs.  If not
++please use
++    reportbug gasic
++to propose enhancements.
++""" % (out,ref))
++    command = "/usr/lib/seqan/bin/mason_simulator illumina --illumina-read-length 10000 -o %s %s"%(out,ref)
+     print("Executing:",command)
      os.system(command)
      # remove the needless SAM file

debian/rules

@@ -3,7 +3,10 @@
 # DH_VERBOSE := 1
 
 %:
-	dh $@ --with python2
+	dh $@ --with python3
+
+override_dh_python3:
+	dh_python3 --shebang=/usr/bin/python3
 
 get-orig-source:
 	. debian/get-orig-source