This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository python-pymummer.
commit 353e651a19b48c8f5bf8cad87f003cb8f0ff2835 Author: Sascha Steinbiss <[email protected]> Date: Tue Nov 15 11:17:46 2016 +0000 New upstream version 0.10.0 --- pymummer/nucmer.py | 5 +++-- pymummer/tests/nucmer_test.py | 7 ++++--- setup.py | 2 +- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/pymummer/nucmer.py b/pymummer/nucmer.py index 1593678..1406189 100644 --- a/pymummer/nucmer.py +++ b/pymummer/nucmer.py @@ -26,6 +26,7 @@ class Runner: snps_header=True, verbose=False, promer=False, + show_snps_C=True, ): self.qry = query self.ref = ref @@ -42,7 +43,7 @@ class Runner: self.snps_header = snps_header self.verbose = verbose self.use_promer = promer - + self.show_snps_C = show_snps_C def _nucmer_command(self, ref, qry, outprefix): @@ -97,7 +98,7 @@ class Runner: def _show_snps_command(self, infile, outfile): - command = 'show-snps -TClr' + command = 'show-snps -T' + ('C' if self.show_snps_C else '') + 'lr' if not self.snps_header: command += ' -H' diff --git a/pymummer/tests/nucmer_test.py b/pymummer/tests/nucmer_test.py index 14d89a0..787fb28 100644 --- a/pymummer/tests/nucmer_test.py +++ b/pymummer/tests/nucmer_test.py @@ -55,11 +55,12 @@ class TestRunner(unittest.TestCase): '''test _show_snps_command''' tests = [ [nucmer.Runner('ref', 'qry', 'outfile', snps_header=False), 'show-snps -TClr -H infile > outfile'], - [nucmer.Runner('ref', 'qry', 'outfile'), 'show-snps -TClr infile > outfile'] + [nucmer.Runner('ref', 'qry', 'outfile'), 'show-snps -TClr infile > outfile'], + [nucmer.Runner('ref', 'qry', 'outfile', show_snps_C=False), 'show-snps -Tlr infile > outfile'] ] - for l in tests: - self.assertEqual(l[0]._show_snps_command('infile', 'outfile'), l[1]) + for nuc_obj, expected in tests: + self.assertEqual(nuc_obj._show_snps_command('infile', 'outfile'), expected) def test_write_script_no_snps(self): diff --git a/setup.py b/setup.py index a779298..db64baf 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,7 @@ if not found_all_progs: setup( name='pymummer', - version='0.9.0', + version='0.10.0', 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 [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
