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commit c6b9f34475790ecee538629bba7a2c2b501b4a77 Author: Sascha Steinbiss <sa...@debian.org> Date: Tue Oct 18 18:36:22 2016 +0000 New upstream version 0.9.0 --- pymummer/nucmer.py | 17 +++++++++++------ pymummer/tests/nucmer_test.py | 5 +++-- setup.py | 2 +- 3 files changed, 15 insertions(+), 9 deletions(-) diff --git a/pymummer/nucmer.py b/pymummer/nucmer.py index a802ab0..1593678 100644 --- a/pymummer/nucmer.py +++ b/pymummer/nucmer.py @@ -20,6 +20,7 @@ class Runner: coords_header=True, diagdiff=None, maxmatch=False, + mincluster=None, simplify=True, show_snps=False, snps_header=True, @@ -35,12 +36,13 @@ class Runner: 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 @@ class Runner: command = 'promer' else: command = 'nucmer' - + command += ' -p ' + outprefix if self.breaklen is not None: @@ -60,7 +62,10 @@ class Runner: 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 @@ class Runner: 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 @@ class Runner: 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 @@ class Runner: 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 index 8962a55..14d89a0 100644 --- a/pymummer/tests/nucmer_test.py +++ b/pymummer/tests/nucmer_test.py @@ -16,6 +16,7 @@ class TestRunner(unittest.TestCase): [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 @@ class TestRunner(unittest.TestCase): 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 @@ class TestRunner(unittest.TestCase): 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 index 2778e8d..a779298 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,7 @@ if not found_all_progs: setup( name='pymummer', - version='0.8.1', + version='0.9.0', description='Wrapper for MUMmer', packages = find_packages(), author='Martin Hunt, Nishadi De Silva', -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pymummer.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit