LICENSE

-Copyright (c) 2014, MarBL
-All rights reserved.
+PURPOSE
+
+Parsnp is a command-line-tool for efficient microbial core genome alignment 
+and SNP detection. Parsnp was designed to work in tandem with Gingr, 
+a flexible platform for visualizing genome alignments and phylogenetic trees; 
+both Parsnp and Gingr form part of the Harvest suite. Parsnp is implemented in C++ and Python.
+
+COPYRIGHT LICENSE
+
+Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+Adam Phillippy
+
+This Software was prepared for the Department of Homeland Security
+(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as
+part of contract HSHQDC-07-C-00020 to manage and operate the National
+Biodefense Analysis and Countermeasures Center (NBACC), a Federally
+Funded Research and Development Center.
 
 Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+modification, are permitted provided that the following conditions are
+met:
 
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
 
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
 
-* Neither the name of the {organization} nor the names of its
+3. Neither the name of the copyright holder nor the names of its
 contributors may be used to endorse or promote products derived from
 this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

build_parsnp_linux.sh

@@ -5,4 +5,6 @@ make install
 cd ..
 ./autogen.sh
 ./configure
+echo "Fix MUSCLE-3.7 linker" 
+make LDADD=-lMUSCLE-3.7
 make install

build_parsnp_osx.sh

@@ -7,4 +7,6 @@ make install
 cd ..
 ./autogen.sh
 ./configure
+echo "Fix MUSCLE-3.7 linker" 
+make LDADD=-lMUSCLE-3.7
 make install

debian/changelog

+parsnp (1.2.1+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.4.1
+
+ -- Andreas Tille <tille@debian.org>  Thu, 14 Nov 2019 11:27:23 +0100
+
 parsnp (1.2+dfsg-6) unstable; urgency=medium
 
   * Use 2to3 to port to Python3

debian/control

@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 12),
                python3-setuptools,
                cython3,
                libmuscle-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/parsnp
 Vcs-Git: https://salsa.debian.org/med-team/parsnp.git
 Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html

debian/patches/proper_calls_to_tools.patch

@@ -49,7 +49,7 @@ Description: Fix path to Debian installed tools
  #set MUMmer paths
  if os.path.exists("%s/MUMmer/nucmer_run"%(PARSNP_DIR)):
      ff = open("%s/MUMmer/nucmer_run"%(PARSNP_DIR))
-@@ -784,12 +770,12 @@ if __name__ == "__main__":
+@@ -789,12 +775,12 @@ if __name__ == "__main__":
      if use_parsnp_mumi and not curated:
          sys.stderr.write( "-->Calculating MUMi..\n")
          if not inifile_exists:
@@ -64,7 +64,7 @@ Description: Fix path to Debian installed tools
          run_command(command)
          try:
              mumif = open(outputDir+os.sep+"all.mumi",'r')
-@@ -962,14 +948,14 @@ if __name__ == "__main__":
+@@ -967,14 +953,14 @@ if __name__ == "__main__":
                  if command == "" and xtrafast and 0:
                      command = "%s/parsnpA_fast %sparsnpAligner.ini"%(PARSNP_DIR,outputDir+os.sep)
                  elif command == "":
@@ -82,7 +82,7 @@ Description: Fix path to Debian installed tools
              run_command(command)
          
  
-@@ -1159,21 +1145,21 @@ if __name__ == "__main__":
+@@ -1164,21 +1150,21 @@ if __name__ == "__main__":
      if xtrafast or 1:
          #add genbank here, if present
          if len(genbank_ref) != 0:
@@ -107,15 +107,15 @@ Description: Fix path to Debian installed tools
  
 -    command = "%s/ft -nt -quote -gamma -slow -boot 100 "%(PARSNP_DIR)+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"
 +    command = "fasttree -nt -quote -gamma -slow -boot 100 "+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"
-     print "-->Reconstructing core genome phylogeny.."
+     print("-->Reconstructing core genome phylogeny..")
      run_command(command)
      #7)reroot to midpoint
-@@ -1204,7 +1190,7 @@ if __name__ == "__main__":
+@@ -1209,7 +1195,7 @@ if __name__ == "__main__":
          if xtrafast or 1:
              #if newick available, add
              #new flag to update branch lengths
 -            run_command("%s/harvest --midpoint-reroot -u -q -i "%(PARSNP_DIR)+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))
 +            run_command("harvesttools --midpoint-reroot -u -q -i "+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))
   
-     print "  |->["+OK_GREEN+"OK"+ENDC+"]"
+     print("  |->["+OK_GREEN+"OK"+ENDC+"]")
  

install.py

 import os,sys,string
 #parsnp basic INSTALL script
 user_home = os.environ["HOME"]
-print "<<Welcome to Parsnp utility script install>>"
+print("<<Welcome to Parsnp utility script install>>")
 
 #check for python version
-if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6):
+if (sys.version_info[0] < 3) or (sys.version_info[0] == 3 and sys.version_info[1] < 1):
     
-    print "Python version is %s. Parsnp requires at least 2.6"%(sys.version)
+    print("Python version is %s. Parsnp requires at least 3.1"%(sys.version))
     sys.exit(1)
 
 #complete shebang

script/shuffle.py

@@ -51,7 +51,7 @@ if __name__ == "__main__":
      rnumber = 0
      shuffleperseq = 1
      if len(sys.argv) < 6:
-         print "\nUsage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>"
+         print("\nUsage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>")
          sys.exit(1)
      else:
          infileName = sys.argv[1]
@@ -77,22 +77,22 @@ if __name__ == "__main__":
          header = infile.readline()
          infiled = infile.read()
          filelen = len(infiled)
-         print "\nInput sequence:%s"%seqfile
-         print "Input sequence length: %d\n"%filelen
+         print("\nInput sequence:%s"%seqfile)
+         print("Input sequence length: %d\n"%filelen)
 
          #split genome into filelen/rsize parts
          partlist = []
          pos = 0
          if rsize > filelen:
              rsize = filelen
-         for part in xrange(0,filelen/rsize):
+         for part in range(0,filelen/rsize):
              partlist.append(infiled[pos:(part+1)*rsize])
              pos +=rsize
 
          partlist.append(infiled[pos:])
 
 
-         for shuffleit in xrange(0,shuffleperseq): 
+         for shuffleit in range(0,shuffleperseq): 
              count = 0
              seq = ""
              parttemp = ""
@@ -114,13 +114,13 @@ if __name__ == "__main__":
                      parttemp = partlist[part1]
                      partlist[part1] = partlist[part2]
                      partlist[part2] = parttemp
-                     print "Transposition"
-                     print "  Positions %d and %d swapped"%(part1,part2)
+                     print("Transposition")
+                     print("  Positions %d and %d swapped"%(part1,part2))
                  elif operation == 2:
                      #inversion
                      partlist[part1] = invertSeq(partlist[part1])
-                     print "Inversion"
-                     print " Position %d"%part1
+                     print("Inversion")
+                     print(" Position %d"%part1)
 
 
                      
@@ -137,7 +137,7 @@ if __name__ == "__main__":
              #write output to file
              fname = seqfile[:-4]
              fname+= "_Shuffled_%d.fna"%(shuffleit+1)
-             print "output: %s"%(fname)
+             print("output: %s"%(fname))
              
              fout = open(fname,'w')
              fout.write(output)