def testRaxml(self):
filename = data_source_path('mafft.anolis.fasta')
alignment = Alignment()
alignment.read_filepath(filename, 'FASTA')
if is_test_enabled(TestLevel.SLOW, _LOG):
self._impl_test_tree_estimator('raxml', datatype="DNA", partitions=[("DNA", 1, 1456)])
def testMultiDnaLocusRun(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
arg_list = ['-d', 'dna',
'--temporaries=%s' % self.ts.top_level_temp,
'--iter-limit=1',
'-m',
'-j', self.job_name,
'-o', self.ts.top_level_temp,
'-i', self.multi_dir,]
self._exe_run_sate(arg_list, rc=0)
seqs_in1_path = os.path.join(self.multi_dir, '1.fasta')
seqs_in2_path = os.path.join(self.multi_dir, '2.fasta')
seqs_out1_path = os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.1.aln')
seqs_out2_path = os.path.join(self.ts.top_level_temp,
self.job_name + '.marker002.2.aln')
self.assertSameInputOutputSequenceData(
[seqs_in1_path, seqs_in2_path],
[seqs_out1_path, seqs_out2_path])
concat_out = os.path.join(self.ts.top_level_temp,
self.job_name + '_temp_iteration_0_seq_alignment.txt')
self.assertSameConcatenatedSequences(
concatenated_data=concat_out,
seq_data_list=[seqs_in1_path, seqs_in2_path])
self.assertNoGapColumns([seqs_out1_path, seqs_out2_path,
concat_out])
def testSmallRna(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
cmd = ['-i', self.small_rna,
'-t', self.small_tree,
'-d', 'rna',
'-o', self.ts.top_level_temp,
'--temporaries=%s' % self.ts.top_level_temp,
'-j', self.job_name,
'--keeptemp',
'--iter-limit=1']
self._exe(cmd)
self.assert_is_nuc(self.small_rna, 'RNA')
self.assert_is_nuc(self.small_aln_path, 'RNA')
self.assertSameInputOutputSequenceData(
[self.small_rna],
[self.small_aln_path])
self.assertNoGapColumns([self.small_aln_path,
self.iter_aln_path])
self.assert_is_nuc(self.iter_aln_path, 'DNA')
self.assertSameSequences([
self.small_rna,
self.small_aln_path,
self.convert_rna_to_dna(self.iter_aln_path, reverse=True)])
cfg = get_configuration(self.cfg_path)
self.assertEqual(cfg.commandline.datatype.upper(), 'RNA')
def testMulti(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
self._main_execution(['-m',
'-i', data_source_path('testmulti'),
'-o', self.ts.top_level_temp,
'--temporaries=%s' % self.ts.top_level_temp,
'-j', self.job_name,
'--iter-limit=1'])
def testHummingBirdDataRun(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
arg_list = ['-d', 'dna',
'--temporaries=%s' % self.ts.top_level_temp,
'--iter-limit=1',
'--start-tree-search-from-current',
'--treefile=%s' % os.path.join(
self.hummingbird_dir,
'starting.tre'),
'--merger=muscle',
'--tree-estimator=fasttree',
'-m',
'-j', self.job_name,
'-o', self.ts.top_level_temp,
'-i', self.hummingbird_dir,]
self._exe_run_sate(arg_list, rc=0)
seqs_in1_path = os.path.join(self.hummingbird_dir,
'AK1.fasta')
seqs_in2_path = os.path.join(self.hummingbird_dir,
'bfib.fasta')
seqs_in3_path = os.path.join(self.hummingbird_dir,
'nd2.fasta')
seqs_in4_path = os.path.join(self.hummingbird_dir,
'nd4.fasta')
seqs_out1_path = os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.AK1.aln')
seqs_out2_path = os.path.join(self.ts.top_level_temp,
self.job_name + '.marker002.bfib.aln')
seqs_out3_path = os.path.join(self.ts.top_level_temp,
self.job_name + '.marker003.nd2.aln')
seqs_out4_path = os.path.join(self.ts.top_level_temp,
self.job_name + '.marker004.nd4.aln')
self.assertSameInputOutputSequenceData(
[seqs_in1_path, seqs_in2_path,
seqs_in3_path, seqs_in4_path],
[seqs_out1_path, seqs_out2_path,
seqs_out3_path, seqs_out4_path])
concat_out = os.path.join(self.ts.top_level_temp,
self.job_name + '_temp_iteration_0_seq_alignment.txt')
self.assertSameConcatenatedSequences(
concatenated_data=concat_out,
seq_data_list=[seqs_in1_path, seqs_in2_path,
seqs_in3_path, seqs_in4_path])
self.assertNoGapColumns([seqs_out1_path, seqs_out2_path,
seqs_out3_path, seqs_out4_path, concat_out])
def testSingleAminoAcidLocusRun(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
arg_list = ['-d', 'protein',
'--temporaries=%s' % self.ts.top_level_temp,
'--iter-limit=1',
'-j', self.job_name,
'-o', self.ts.top_level_temp,
'-i', self.caenophidia_file,]
self._exe_run_sate(arg_list, rc=0)
self.assertSameInputOutputSequenceData(
[self.caenophidia_file],
[os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.caenophidia_mos.aln')])
self.assertNoGapColumns([os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.caenophidia_mos.aln')])
def testRnaDnaIdentity(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
dna_cmd = ['-i', self.dna,
'-d', 'dna',
'-t', self.tree,
'-o', self.dna_tmp,
'--temporaries=%s' % self.dna_tmp,
'-j', self.job_name,
'--aligner=mafft',
'--merger=muscle',
'--tree-estimator=fasttree',
'--start-tree-search-from-current',
'--tree-estimator-model=-gtr -gamma -seed 1111',
'--iter-limit=1']
self._exe_run_sate(dna_cmd)
rna_cmd = ['-i', self.rna,
'-d', 'rna',
'-t', self.tree,
'-o', self.rna_tmp,
'--temporaries=%s' % self.rna_tmp,
'-j', self.job_name,
'--aligner=mafft',
'--merger=muscle',
'--tree-estimator=fasttree',
'--start-tree-search-from-current',
'--tree-estimator-model=-gtr -gamma -seed 1111',
'--iter-limit=1']
self._exe_run_sate(rna_cmd)
self.assert_is_nuc(self.dna_aln, 'DNA')
self.assert_is_nuc(self.rna_aln, 'RNA')
self.assertNoGapColumns([
self.dna_aln,
self.rna_aln])
self.assertSameDataSet([
self.rna,
self.rna_aln,
self.convert_rna_to_dna(self.dna, reverse=True),
self.convert_rna_to_dna(self.dna_aln, reverse=True)])
# self.assertSameScores([self.dna_score, self.rna_score])
# self.assertSameTrees([self.dna_tree, self.rna_tree])
self.assertSameFiles([self.dna_tmp_aln, self.rna_tmp_aln])
def testProteinAmbiguousCharactersMafftFasttreeTrusted(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
arg_list = ['-d', 'protein',
'--temporaries=%s' % self.ts.top_level_temp,
'--iter-limit=1',
'-j', self.job_name,
'-o', self.ts.top_level_temp,
'-i', self.ambig_aa,
'-t', self.ambig_aa_tree,
'--aligner=mafft',
'--merger=muscle',
'--tree-estimator=fasttree',]
self._exe_run_sate(arg_list, rc=0)
self.assertSameInputOutputSequenceData(
[self.ambig_aa],
[os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.caenophidia_mos.ambiguities.aln')])
self.assertNoGapColumns([os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.caenophidia_mos.ambiguities.aln')])
def testDnaAmbiguousCharactersClustalRaxmlUntrusted(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG,
module_name=".".join([self.__class__.__name__,
sys._getframe().f_code.co_name])):
arg_list = ['-d', 'dna',
'--temporaries=%s' % self.ts.top_level_temp,
'--iter-limit=1',
'-j', self.job_name,
'-o', self.ts.top_level_temp,
'-i', self.ambig_dna,
'-t', self.ambig_dna_tree,
'--aligner=clustalw2',
'--merger=muscle',
'--tree-estimator=raxml',
'--untrusted',]
self._exe_run_sate(arg_list, rc=0)
self.assertSameInputOutputSequenceData(
[self.ambig_dna],
[os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.small.ambiguities.aln')])
self.assertNoGapColumns([os.path.join(self.ts.top_level_temp,
self.job_name + '.marker001.small.ambiguities.aln')])
def testMuscle(self):
if is_test_enabled(TestLevel.SLOW, _LOG):
self._impl_test_merger('muscle')
def testOpal(self):
if is_test_enabled(TestLevel.SLOW, _LOG):
self._impl_test_merger('opal')
def testMulti(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._main_execution(['-m', '-i', data_source_path('testmulti'), '--iter-limit=1'])
def testOpal(self):
if is_test_enabled(TestLevel.SLOW, _LOG):
self._impl_test_merger('opal')
def testOpal(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._impl_test_aligner('opal', 'anolis.fasta')
def testClustalW2(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._impl_test_aligner('clustalw2', 'anolis.fasta')
def testClustalW2(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._impl_test_aligner('clustalw2', 'anolis.fasta')
def testOpal(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._impl_test_aligner('opal', 'anolis.fasta')
def testMafft(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._impl_test_aligner('mafft', 'anolis.fasta')
def testMafft(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._impl_test_aligner('mafft', 'anolis.fasta')
def testMuscle(self):
if is_test_enabled(TestLevel.SLOW, _LOG):
self._impl_test_merger('muscle')
def testBasic(self):
if is_test_enabled(TestLevel.EXHAUSTIVE, _LOG):
self._main_execution(['--hep'], rc=2)
self._main_execution([], rc=1)
self._main_execution(['--help'], rc=0)
