def test_recombination_convergence(self):
parser = self.default_arg_parse()
gubbins_runner = common.GubbinsCommon(
parser.parse_args([
"--converge_method", "recombination", "--iterations", '15',
'--no_cleanup',
'gubbins/tests/data/multiple_recombinations.aln'
]))
gubbins_runner.parse_and_run()
assert common.GubbinsCommon.have_recombinations_been_seen_before(
'multiple_recombinations.recombination_predictions.embl', [
'RAxML_result.multiple_recombinations.iteration_1.tab',
'RAxML_result.multiple_recombinations.iteration_2.tab',
'RAxML_result.multiple_recombinations.iteration_3.tab',
'RAxML_result.multiple_recombinations.iteration_4.tab',
'RAxML_result.multiple_recombinations.iteration_5.tab',
'RAxML_result.multiple_recombinations.iteration_6.tab',
'RAxML_result.multiple_recombinations.iteration_7.tab',
'RAxML_result.multiple_recombinations.iteration_8.tab',
'RAxML_result.multiple_recombinations.iteration_9.tab',
'RAxML_result.multiple_recombinations.iteration_10.tab',
'RAxML_result.multiple_recombinations.iteration_11.tab',
'RAxML_result.multiple_recombinations.iteration_12.tab',
'RAxML_result.multiple_recombinations.iteration_13.tab',
'RAxML_result.multiple_recombinations.iteration_14.tab',
'RAxML_result.multiple_recombinations.iteration_15.tab'
]) == 1
self.cleanup()
def test_rename_final_output(self):
parser = self.default_arg_parse()
gubbins_runner = common.GubbinsCommon(
parser.parse_args([
"--prefix", "different_prefix",
'gubbins/tests/data/multiple_recombinations.aln'
]))
gubbins_runner.parse_and_run()
assert os.path.exists(
'different_prefix.summary_of_snp_distribution.vcf')
assert os.path.exists(
'different_prefix.recombination_predictions.embl')
assert os.path.exists('different_prefix.per_branch_statistics.csv')
assert os.path.exists(
'different_prefix.filtered_polymorphic_sites.fasta')
assert os.path.exists(
'different_prefix.filtered_polymorphic_sites.phylip')
assert os.path.exists('different_prefix.recombination_predictions.gff')
assert os.path.exists(
'different_prefix.branch_base_reconstruction.embl')
assert os.path.exists('different_prefix.final_tree.tre')
assert os.path.exists('different_prefix.node_labelled.final_tree.tre')
self.cleanup()
def test_robinson_foulds_convergence(self):
self.cleanup()
parser = self.default_arg_parse()
gubbins_runner = common.GubbinsCommon(
parser.parse_args([
"--converge_method", "robinson_foulds", "--iterations", '15',
'--no_cleanup',
'gubbins/tests/data/multiple_recombinations.aln'
]))
gubbins_runner.parse_and_run()
assert common.GubbinsCommon.has_tree_been_seen_before([
'RAxML_result.multiple_recombinations.iteration_1',
'RAxML_result.multiple_recombinations.iteration_2',
'RAxML_result.multiple_recombinations.iteration_3',
'RAxML_result.multiple_recombinations.iteration_4',
'RAxML_result.multiple_recombinations.iteration_5',
'RAxML_result.multiple_recombinations.iteration_6',
'RAxML_result.multiple_recombinations.iteration_7',
'RAxML_result.multiple_recombinations.iteration_8',
'RAxML_result.multiple_recombinations.iteration_9',
'RAxML_result.multiple_recombinations.iteration_10',
'multiple_recombinations.final_tree.tre'
], 'robinson_foulds') == 1
self.cleanup()
def test_parse_and_run(self):
parser = self.default_arg_parse()
# multiple recombinations
gubbins_runner = common.GubbinsCommon(
parser.parse_args(
['gubbins/tests/data/multiple_recombinations.aln']))
gubbins_runner.parse_and_run()
assert not os.path.exists('multiple_recombinations.aln.start')
assert not os.path.exists(
'RAxML_result.multiple_recombinations.iteration_5.ancestor.tre')
assert not os.path.exists(
'RAxML_result.multiple_recombinations.iteration_5.seq.joint.txt')
assert not os.path.exists(
'RAxML_result.multiple_recombinations.iteration_5.prob.joint.txt')
assert not os.path.exists('log.txt')
assert not os.path.exists('latest_tree.multiple_recombinations.tre')
self.cleanup()
def test_change_window_size(self):
parser = self.base_arg_parse()
parser.add_argument('--min_window_size',
'-a',
help='Minimum window size, default 100',
type=int,
default=80)
parser.add_argument('--max_window_size',
'-b',
help='Maximum window size, default 10000',
type=int,
default=1000)
gubbins_runner = common.GubbinsCommon(
parser.parse_args([
"--prefix", "different_prefix",
'gubbins/tests/data/multiple_recombinations.aln'
]))
gubbins_runner.parse_and_run()
assert os.path.exists(
'different_prefix.summary_of_snp_distribution.vcf')
assert os.path.exists(
'different_prefix.recombination_predictions.embl')
assert os.path.exists('different_prefix.per_branch_statistics.csv')
assert os.path.exists(
'different_prefix.filtered_polymorphic_sites.fasta')
assert os.path.exists(
'different_prefix.filtered_polymorphic_sites.phylip')
assert os.path.exists('different_prefix.recombination_predictions.gff')
assert os.path.exists(
'different_prefix.branch_base_reconstruction.embl')
assert os.path.exists('different_prefix.final_tree.tre')
assert os.path.exists('different_prefix.node_labelled.final_tree.tre')
self.cleanup()
def test_parse_and_run(self):
parser = argparse.ArgumentParser(
description='Iteratively detect recombinations')
parser.add_argument('alignment_filename',
help='Multifasta alignment file')
parser.add_argument('--outgroup',
'-o',
help='Outgroup name for rerooting')
parser.add_argument('--starting_tree', '-s', help='Starting tree')
parser.add_argument('--use_time_stamp',
'-u',
action='count',
help='Use a time stamp in file names')
parser.add_argument('--verbose',
'-v',
action='count',
help='Turn on debugging',
default=0)
parser.add_argument('--no_cleanup',
'-n',
action='count',
help='Dont cleanup intermediate files')
parser.add_argument(
'--tree_builder',
'-t',
help=
'Application to use for tree building (raxml, fasttree, hybrid), default RAxML',
default="raxml")
parser.add_argument('--iterations',
'-i',
help='Maximum No. of iterations, default is 5',
type=int,
default=5)
parser.add_argument(
'--min_snps',
'-m',
help='Min SNPs to identify a recombination block, default is 3',
type=int,
default=3)
parser.add_argument(
'--filter_percentage',
'-f',
help=
'Filter out taxa with more than this percentage of gaps, default is 25',
type=int,
default=15)
parser.add_argument('--prefix',
'-p',
help='Add a prefix to the final output filenames')
parser.add_argument(
'--threads',
'-c',
help=
'Number of threads to run with RAXML, but only if a PTHREADS version is available',
type=int,
default=1)
parser.add_argument(
'--converge_method',
'-z',
help=
'Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]',
default='weighted_robinson_foulds')
parser.add_argument('--min_window_size',
'-a',
help='Minimum window size, default 100',
type=int,
default=100)
parser.add_argument('--max_window_size',
'-b',
help='Maximum window size, default 10000',
type=int,
default=10000)
# multiple recombinations
gubbins_runner = common.GubbinsCommon(
parser.parse_args(
['gubbins/tests/data/multiple_recombinations.aln']))
gubbins_runner.parse_and_run()
assert not os.path.exists('multiple_recombinations.aln.start')
assert not os.path.exists(
'RAxML_result.multiple_recombinations.iteration_5.ancestor.tre')
assert not os.path.exists(
'RAxML_result.multiple_recombinations.iteration_5.seq.joint.txt')
assert not os.path.exists(
'RAxML_result.multiple_recombinations.iteration_5.prob.joint.txt')
assert not os.path.exists('log.txt')
assert not os.path.exists('latest_tree.multiple_recombinations.tre')
os.remove('multiple_recombinations.summary_of_snp_distribution.vcf')
os.remove('multiple_recombinations.recombination_predictions.embl')
os.remove('multiple_recombinations.per_branch_statistics.csv')
os.remove('multiple_recombinations.filtered_polymorphic_sites.fasta')
os.remove('multiple_recombinations.filtered_polymorphic_sites.phylip')
os.remove('multiple_recombinations.recombination_predictions.gff')
os.remove('multiple_recombinations.branch_base_reconstruction.embl')
os.remove('multiple_recombinations.final_tree.tre')
os.remove('multiple_recombinations.node_labelled.tre')
def test_robinson_foulds_convergence(self):
parser = argparse.ArgumentParser(
description='Iteratively detect recombinations')
parser.add_argument('alignment_filename',
help='Multifasta alignment file')
parser.add_argument('--outgroup',
'-o',
help='Outgroup name for rerooting')
parser.add_argument('--starting_tree', '-s', help='Starting tree')
parser.add_argument('--use_time_stamp',
'-u',
action='count',
help='Use a time stamp in file names')
parser.add_argument('--verbose',
'-v',
action='count',
help='Turn on debugging',
default=0)
parser.add_argument('--no_cleanup',
'-n',
action='count',
help='Dont cleanup intermediate files')
parser.add_argument(
'--tree_builder',
'-t',
help=
'Application to use for tree building (raxml, fasttree, hybrid), default RAxML',
default="raxml")
parser.add_argument('--iterations',
'-i',
help='Maximum No. of iterations, default is 5',
type=int,
default=5)
parser.add_argument(
'--min_snps',
'-m',
help='Min SNPs to identify a recombination block, default is 3',
type=int,
default=3)
parser.add_argument(
'--filter_percentage',
'-f',
help=
'Filter out taxa with more than this percentage of gaps, default is 25',
type=int,
default=15)
parser.add_argument('--prefix',
'-p',
help='Add a prefix to the final output filenames')
parser.add_argument(
'--threads',
'-c',
help=
'Number of threads to run with RAXML, but only if a PTHREADS version is available',
type=int,
default=1)
parser.add_argument(
'--converge_method',
'-z',
help=
'Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]',
default='weighted_robinson_foulds')
parser.add_argument('--min_window_size',
'-a',
help='Minimum window size, default 100',
type=int,
default=100)
parser.add_argument('--max_window_size',
'-b',
help='Maximum window size, default 10000',
type=int,
default=10000)
gubbins_runner = common.GubbinsCommon(
parser.parse_args([
"--converge_method", "robinson_foulds", "--iterations", '15',
'--no_cleanup',
'gubbins/tests/data/multiple_recombinations.aln'
]))
gubbins_runner.parse_and_run()
assert common.GubbinsCommon.has_tree_been_seen_before([
'RAxML_result.multiple_recombinations.iteration_1',
'RAxML_result.multiple_recombinations.iteration_2',
'RAxML_result.multiple_recombinations.iteration_3',
'RAxML_result.multiple_recombinations.iteration_4',
'RAxML_result.multiple_recombinations.iteration_5',
'RAxML_result.multiple_recombinations.iteration_6',
'RAxML_result.multiple_recombinations.iteration_7',
'RAxML_result.multiple_recombinations.iteration_8',
'RAxML_result.multiple_recombinations.iteration_9',
'RAxML_result.multiple_recombinations.iteration_10',
'multiple_recombinations.final_tree.tre'
], 'robinson_foulds') == 1
os.remove('log.txt')
r = glob.glob("RAxML_*")
for i in r:
os.remove(i)
r = glob.glob("multiple_recombinations.aln.*")
for i in r:
os.remove(i)
help='Criteria to use to know when to halt iterations',
default='weighted_robinson_foulds',
choices=['weighted_robinson_foulds', 'robinson_foulds', 'recombination'])
parser.add_argument('--version',
action='version',
version=str(
pkg_resources.get_distribution("gubbins").version))
parser.add_argument('--min_window_size',
'-a',
help='Minimum window size',
type=int,
default=100)
parser.add_argument('--max_window_size',
'-b',
help='Maximum window size',
type=int,
default=10000)
parser.add_argument('--raxml_model',
'-r',
help='RAxML model',
default='GTRCAT',
choices=['GTRGAMMA', 'GTRCAT'])
parser.add_argument('--remove_identical_sequences',
'-d',
action='count',
help='Remove identical sequences',
default=0)
gubbins_runner = common.GubbinsCommon(parser.parse_args())
gubbins_runner.parse_and_run()
