Merge pull request #23 from martinghunt/expose_mincluster

Expose mincluster
sanger-pathogens · Oct 17, 2016 · 3c1dee6 · 3c1dee6
2 parents e25a59e + b352fa6
commit 3c1dee6
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Showing 3 changed files with 15 additions and 9 deletions.
diff --git a/pymummer/nucmer.py b/pymummer/nucmer.py
@@ -20,6 +20,7 @@ def __init__(
       coords_header=True,
       diagdiff=None,
       maxmatch=False,
+      mincluster=None,
       simplify=True,
       show_snps=False,
       snps_header=True,
@@ -35,12 +36,13 @@ def __init__(
         self.diagdiff = diagdiff
         self.coords_header = coords_header
         self.maxmatch = maxmatch
+        self.mincluster = mincluster
         self.simplify = simplify
         self.show_snps = show_snps
         self.snps_header = snps_header
         self.verbose = verbose
         self.use_promer = promer
-    
+
 
 
     def _nucmer_command(self, ref, qry, outprefix):
@@ -49,7 +51,7 @@ def _nucmer_command(self, ref, qry, outprefix):
             command = 'promer'
         else:
             command = 'nucmer'
-  
+
         command += ' -p ' + outprefix
 
         if self.breaklen is not None:
@@ -60,7 +62,10 @@ def _nucmer_command(self, ref, qry, outprefix):
 
         if self.maxmatch:
             command += ' --maxmatch'
-
+
+        if self.mincluster is not None:
+            command += ' -c ' + str(self.mincluster)
+
         if not self.simplify and not self.use_promer:
         	command += ' --nosimplify'
 
@@ -79,7 +84,7 @@ def _delta_filter_command(self, infile, outfile):
             command += ' -l ' + str(self.min_length)
 
         return command + ' ' + infile + ' > ' + outfile
-        
+
 
     def _show_coords_command(self, infile, outfile):
         '''Construct show-coords command'''
@@ -109,7 +114,7 @@ def _write_script(self, script_name, ref, qry, outfile):
         if self.show_snps:
             print(self._show_snps_command('p.delta.filter', outfile + '.snps'), file=f)
         pyfastaq.utils.close(f)
-    
+
 
     def run(self):
         '''
@@ -125,7 +130,7 @@ def run(self):
         original_dir = os.getcwd()
         os.chdir(tmpdir)
         script = 'run_nucmer.sh'
-        self._write_script(script, ref, qry, outfile) 
+        self._write_script(script, ref, qry, outfile)
         syscall.run('bash ' + script, verbose=self.verbose)
         os.chdir(original_dir)
         shutil.rmtree(tmpdir)

diff --git a/pymummer/tests/nucmer_test.py b/pymummer/tests/nucmer_test.py
@@ -16,6 +16,7 @@ def test_nucmer_command(self):
             [nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11), 'nucmer -p pre -D 11 ref qry'],
             [nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11, promer=True), 'promer -p pre ref qry'],
             [nucmer.Runner('ref', 'qry', 'outfile', maxmatch=True), 'nucmer -p pre --maxmatch ref qry'],
+            [nucmer.Runner('ref', 'qry', 'outfile', mincluster=42), 'nucmer -p pre -c 42 ref qry'],
             [nucmer.Runner('ref', 'qry', 'outfile', simplify=False), 'nucmer -p pre --nosimplify ref qry'],
             [nucmer.Runner('ref', 'qry', 'outfile', promer=True), 'promer -p pre ref qry'],
             [nucmer.Runner('ref', 'qry', 'outfile', promer=True, breaklen=42), 'promer -p pre -b 42 ref qry'],
@@ -37,7 +38,7 @@ def test_delta_filter_command(self):
 
         for l in tests:
             self.assertEqual(l[0]._delta_filter_command('infile', 'outfile'), l[1])
-        
+
 
     def test_show_coords_command(self):
         '''test _show_coords_command'''
@@ -93,5 +94,5 @@ def test_run_nucmer(self):
         self.assertTrue(filecmp.cmp(tmp_out + '.snps', expected + '.snps', shallow=False))
         os.unlink(tmp_out)
         os.unlink(tmp_out + '.snps')
-        
+
 
diff --git a/setup.py b/setup.py
@@ -26,7 +26,7 @@
 
 setup(
     name='pymummer',
-    version='0.8.1',
+    version='0.9.0',
     description='Wrapper for MUMmer',
     packages = find_packages(),
     author='Martin Hunt, Nishadi De Silva',