def setUp(self):
super().setUp()
tests = ('blastp', 'WP_009885814.faa')
self.blast = (tests[0], get_data_path(tests[1]),
_get_named_data_path('%s.diamond' % tests[1]))
seqs = skbio.read(_get_named_data_path('cache.faa'), format='fasta')
self.cache = DiamondCache(list(seqs))
def setUp(self):
self.tmp_dir = mkdtemp()
self.db_fp = 'tigrfam_v15.0.db'
self.obs_db_fp = join(self.tmp_dir, self.db_fp)
self.exp_db_fp = _get_named_data_path(self.db_fp)
self.d = dirname(self.exp_db_fp)
self.pressed_fp = 'tigrfam_v15.0.hmm.h3f'
self.obs_pressed_fp = join(self.tmp_dir, self.pressed_fp)
self.exp_pressed_fp = _get_named_data_path(self.pressed_fp)
def setUp(self):
self.tmp_dir = mkdtemp()
self.db_fp = 'tigrfam_v15.0.db'
self.obs_db_fp = join(self.tmp_dir, self.db_fp)
self.exp_db_fp = _get_named_data_path(self.db_fp)
self.d = dirname(self.exp_db_fp)
self.pressed_fp = 'tigrfam_v15.0.hmm.h3f'
self.obs_pressed_fp = join(self.tmp_dir, self.pressed_fp)
self.exp_pressed_fp = _get_named_data_path(self.pressed_fp)
def setUp(self):
self.tmp_dir = mkdtemp()
self.positive_fps = [_get_named_data_path(i) for i in [
# modified from NC_018498.gbk
'NC_018498_partial_1.gbk',
'NC_018498_partial_1.gbk',
'NC_018498_partial_2.gbk',
]]
self.positive_params = [
{'-p': 'meta'},
{'-p': 'meta', '-f': 'gff'},
{'-p': 'single'}]
self.positive_suffices = [
{'-o': 'gbk', '-a': 'faa', '-d': 'fna'},
{'-o': 'gff', '-a': 'faa', '-d': 'fna'},
{'-o': 'gbk', '-a': 'faa', '-d': 'fna'}]
self.positive_outdir = [
'test_1',
'test_2',
'test_3']
self.negative_fps = [get_data_path(i) for i in [
'empty',
'whitespace_only']]
self.parse_fp = _get_named_data_path('parse_test.faa')
self.parse_exp = [
{Feature(type_='CDS',
id='1_1',
right_partial_=False,
left_partial_=False,
location='686..1828',
translation='MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNEYFSVKCNLNKYFLITSKSEPELKQILVPSR*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.236"',
rc_=False): [(685, 1828)],
Feature(type_='CDS',
id='1_2',
location='1828..>2757',
translation='MNLYDLLELPTTASIKEIKIAYKRLAKRYHPDVNKLGSQTFVEINNAYSILSDPNQKEKYFNYKTQHFID',
right_partial_=True,
left_partial_=False,
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.271"',
rc_=False): [(1827, 2757)]},
{Feature(type_='CDS',
id='2_1',
location='21577..22128',
right_partial_=False,
left_partial_=False,
translation='MKKTSPFILRRTKNKVLKELPKKIITDIYVELSEEHQKLYDKQKTDGLKEIKESDAKNALFDV*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.272"',
rc_=False): [(21576, 22128)]}]
def setUp(self):
super().setUp()
cases = [('blastp', 'WP_009885814.faa'),
('blastx', 'WP_009885814.fna')]
Test = namedtuple('Test', ['aligner', 'input', 'exp'])
self.tests = [
Test(i[0], get_data_path(i[1]),
_get_named_data_path('%s.diamond' % i[1])) for i in cases
]
seqs = skbio.read(_get_named_data_path('cache.faa'), format='fasta')
self.cache = DiamondCache(list(seqs))
def setUp(self):
super().setUp()
suffices = ['tblout']
Files = namedtuple('Files', suffices)
Case = namedtuple('Case', ['query', 'obs', 'exp'])
self.cases = []
for f in ['Pfam_B_1.faa']:
fns = ['{}.{}'.format(f, s) for s in suffices]
obs_files = Files(*[join(self.tmp_dir, fn) for fn in fns])
exp_files = Files(*[_get_named_data_path(fn) for fn in fns])
self.cases.append(
Case(_get_named_data_path(f), obs_files, exp_files))
def setUp(self):
super().setUp()
cases = [('blastp', 'WP_009885814.faa'),
('blastx', 'WP_009885814.fna')]
Test = namedtuple('Test', ['aligner', 'input', 'exp'])
self.tests = [Test(i[0],
get_data_path(i[1]),
_get_named_data_path('%s.diamond' % i[1]))
for i in cases]
seqs = skbio.read(_get_named_data_path('cache.faa'), format='fasta')
self.cache = DiamondCache(list(seqs))
def setUp(self):
self.parse_fp = _get_named_data_path('parse_test.faa')
self.parse_exp = [{
Feature(type_='CDS',
id='1_1',
right_partial_=False,
left_partial_=False,
location='686..1828',
translation='MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNEYFSVKCNLNKYFLITSKSEPELKQILVPSR*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.236"',
rc_=False): [(685, 1828)],
Feature(type_='CDS',
id='1_2',
location='1828..>2757',
translation='MNLYDLLELPTTASIKEIKIAYKRLAKRYHPDVNKLGSQTFVEINNAYSILSDPNQKEKYFNYKTQHFID',
right_partial_=True,
left_partial_=False,
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.271"',
rc_=False): [(1827, 2757)]
}, {
Feature(type_='CDS',
id='2_1',
location='21577..22128',
right_partial_=False,
left_partial_=False,
translation='MKKTSPFILRRTKNKVLKELPKKIITDIYVELSEEHQKLYDKQKTDGLKEIKESDAKNALFDV*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.272"',
rc_=False): [(21576, 22128)]
}]
def setUp(self):
self.tmp_dir = mkdtemp()
self.negative_fps = [
get_data_path(i) for i in ['empty', 'whitespace_only']
]
Case = namedtuple('Case', ['query', 'kwargs', 'outdir'])
self.cases = [
Case(i, j, k) for i, j, k in zip(
[
_get_named_data_path(i) for i in
# modified from NC_018498.gbk
[
'NC_018498_partial_1.gbk', 'NC_018498_partial_1.gbk',
'NC_018498_partial_2.gbk'
]
],
[{
'-p': 'meta',
'-f': 'gbk'
}, {
'-p': 'meta'
}, {
'-p': 'single'
}],
['test_1', 'test_2', 'test_3'])
]
def test_run(self):
# taken from MinCED test files
fn = 'Aquifex_aeolicus_VF5.fna'
query = _get_named_data_path(fn)
exp = splitext(query)[0]
params = [{
'-searchWL': '8',
'gff': True,
'gffFull': False,
'spacers': False
}, {
'-searchWL': '8',
'-minNR': '3',
'gffFull': True,
'gff': False,
'spacers': False
}, {
'gff': True,
'spacers': True,
'gffFull': False
}]
exp_fps = ['.gff', '.gffFull', '.gff']
for param, s in zip(params, exp_fps):
res = run(query, self.tmp_dir, **param)
self.assertTrue(cmp(res.params['out'].value, exp + s))
def setUp(self):
self.parse_fp = _get_named_data_path('parse_test.faa')
self.parse_exp = [
{Feature(type_='CDS',
id='1_1',
right_partial_=False,
left_partial_=False,
location='686..1828',
translation='MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNEYFSVKCNLNKYFLITSKSEPELKQILVPSR*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.236"',
rc_=False): [(685, 1828)],
Feature(type_='CDS',
id='1_2',
location='1828..>2757',
translation='MNLYDLLELPTTASIKEIKIAYKRLAKRYHPDVNKLGSQTFVEINNAYSILSDPNQKEKYFNYKTQHFID',
right_partial_=True,
left_partial_=False,
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.271"',
rc_=False): [(1827, 2757)]},
{Feature(type_='CDS',
id='2_1',
location='21577..22128',
right_partial_=False,
left_partial_=False,
translation='MKKTSPFILRRTKNKVLKELPKKIITDIYVELSEEHQKLYDKQKTDGLKEIKESDAKNALFDV*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.272"',
rc_=False): [(21576, 22128)]}]
def setUp(self):
super().setUp()
tests = [('blastp', 'WP_009885814.faa'),
('blastx', 'WP_009885814.fna')]
self.blast = [
(i[0], get_data_path(i[1]),
_get_named_data_path('%s.diamond' % i[1]))
for i in tests]
def test_run(self):
for case in self.cases:
exp_d = _get_named_data_path(case.outdir)
obs_d = join(self.tmp_dir, case.outdir)
run(case.query, obs_d, **case.kwargs)
for f in listdir(exp_d):
self.assertTrue(
cmp(join(obs_d, f), join(exp_d, f), shallow=False))
def setUp(self):
super().setUp()
cases = [('blastp', 'WP_009885814.faa'),
('blastx', 'WP_009885814.fna')]
Test = namedtuple('Test', ['aligner', 'input', 'exp'])
self.tests = [
Test(i[0], get_data_path(i[1]), _get_named_data_path(i[1]))
for i in cases
]
def setUp(self):
super().setUp()
cases = [('blastp', 'WP_009885814.faa'),
('blastx', 'WP_009885814.fna')]
Test = namedtuple('Test', ['aligner', 'input', 'exp'])
self.tests = [Test(i[0],
get_data_path(i[1]),
_get_named_data_path(i[1]))
for i in cases]
def _test_eq(self):
for fp in self.uniref_res:
for suffix in ['fasta', 'dmnd']:
fp = '.'.join([fp, suffix])
obs = join(self.tmp_dir, fp)
exp = _get_named_data_path(fp)
if exists(exp):
with open(obs) as o, open(exp) as e:
self.assertEqual(o.read(), e.read())
remove(obs)
def setUp(self):
self.tmp_dir = mkdtemp()
self.faa = _get_named_data_path('db.faa')
self.obs_db = join(self.tmp_dir, 'db.dmnd')
self.exp_db = _get_named_data_path('db.dmnd')
cases = [['blastp', 'test.faa']]
# ['blastx', 'test.fna']]
suffices = ['daa', 'tab', 'sam', 'sam_df', 'sam_best', 'sam_io5', 'sam_io12']
Files = namedtuple('Files', suffices)
Case = namedtuple('Case', ['aligner', 'query', 'obs', 'exp'])
self.cases = []
for b, f in cases:
fns = ['{}.{}'.format(f, s) for s in suffices]
obs_files = Files(*[join(self.tmp_dir, fn) for fn in fns])
exp_files = Files(*[_get_named_data_path(fn) for fn in fns])
self.cases.append(Case(b, _get_named_data_path(f), obs_files, exp_files))
self.neg_fp = [get_data_path(i) for i in
['empty', 'whitespace_only']]
def test_pred_run(self):
for fp, params, outdir in zip(self.positive_fps, self.positive_params,
self.positive_outdir):
exp_d = _get_named_data_path(outdir)
obs_d = join(self.tmp_dir, outdir)
pred = FeaturePred(None, obs_d)
res = pred.run(fp, params)
self.assertEqual(res['ExitStatus'], 0)
for f in listdir(exp_d):
self.assertTrue(
cmp(join(obs_d, f), join(exp_d, f), shallow=False))
res['StdOut'].close()
res['StdErr'].close()
def test_pred_run(self):
for fp, params, outdir in zip(self.positive_fps,
self.positive_params,
self.positive_outdir):
exp_d = _get_named_data_path(outdir)
obs_d = join(self.tmp_dir, outdir)
pred = FeaturePred(None, obs_d)
res = pred.run(fp, params)
self.assertEqual(res['ExitStatus'], 0)
for f in listdir(exp_d):
self.assertTrue(
cmp(join(obs_d, f), join(exp_d, f), shallow=False))
res['StdOut'].close()
res['StdErr'].close()
def setUp(self):
self.tmp_dir = mkdtemp()
self.faa = _get_named_data_path('db.faa')
self.obs_db = join(self.tmp_dir, 'db.dmnd')
self.exp_db = _get_named_data_path('db.dmnd')
cases = [['blastp', 'test.faa']]
# ['blastx', 'test.fna']]
suffices = [
'daa', 'tab', 'sam', 'sam_df', 'sam_best', 'sam_io5', 'sam_io12'
]
Files = namedtuple('Files', suffices)
Case = namedtuple('Case', ['aligner', 'query', 'obs', 'exp'])
self.cases = []
for b, f in cases:
fns = ['{}.{}'.format(f, s) for s in suffices]
obs_files = Files(*[join(self.tmp_dir, fn) for fn in fns])
exp_files = Files(*[_get_named_data_path(fn) for fn in fns])
self.cases.append(
Case(b, _get_named_data_path(f), obs_files, exp_files))
self.neg_fp = [get_data_path(i) for i in ['empty', 'whitespace_only']]
def test_run(self):
# taken from MinCED test files
fn = 'Aquifex_aeolicus_VF5.fna'
query = _get_named_data_path(fn)
exp = splitext(query)[0]
params = [
{'-searchWL': '8', 'gff': True, 'gffFull': False, 'spacers': False},
{'-searchWL': '8', '-minNR': '3', 'gffFull': True, 'gff': False, 'spacers': False},
{'gff': True, 'spacers': True, 'gffFull': False}]
exp_fps = ['.gff', '.gffFull', '.gff']
for param, s in zip(params, exp_fps):
res = run(query, self.tmp_dir, **param)
self.assertTrue(
cmp(res.params['out'].value, exp + s))
def setUp(self):
self.tmp_dir = mkdtemp()
self.db_fp = 'uniprotkb.db'
self.obs_db_fp = join(self.tmp_dir, self.db_fp)
self.exp_db_fp = _get_named_data_path(self.db_fp)
self.uniprotkb = [_get_named_data_path('uniprot_sprot.xml.gz'),
_get_named_data_path('uniprot_trembl.xml.gz'),
12]
self.d = dirname(self.exp_db_fp)
self.uniref_fp = _get_named_data_path('uniref100.fasta.gz')
self.uniref_res = [
'Swiss-Prot_Archaea',
'Swiss-Prot_Bacteria',
'Swiss-Prot_Viruses',
'Swiss-Prot_Eukaryota',
'Swiss-Prot_other',
'TrEMBL_Archaea',
'TrEMBL_Bacteria',
'TrEMBL_Viruses',
'TrEMBL_Eukaryota',
'TrEMBL_other',
'_other']
def setUp(self):
self.tmp_dir = mkdtemp()
self.negative_fps = [get_data_path(i) for i in
['empty', 'whitespace_only']]
Case = namedtuple('Case', ['query', 'kwargs', 'outdir'])
self.cases = [Case(i, j, k) for i, j, k in
zip([_get_named_data_path(i) for i in
# modified from NC_018498.gbk
['NC_018498_partial_1.gbk',
'NC_018498_partial_1.gbk',
'NC_018498_partial_2.gbk']],
[{'-p': 'meta', '-f': 'gbk'},
{'-p': 'meta'},
{'-p': 'single'}],
['test_1',
'test_2',
'test_3'])]
def setUp(self):
tests = [('blastp', 'WP_009885814.faa'),
('blastx', 'WP_009885814.fna')]
self.blast = [
(i[0],
get_data_path(i[1]),
_get_named_data_path(('%s.sam' % i[1])))
for i in tests]
self.exp = \
pd.DataFrame({
'sseqid': ['UniRef100_P47599', 'UniRef100_B2HPZ3',
'UniRef100_A4T166'],
'evalue': [2.1e-229, 2.9e-58, 3.3e-57],
'bitscore': [2009, 533, 524],
'sequence': [
'MQSHKILVVNAGSSSIKFQLFNDKKQVLAKGLCERIFIDGFFKLEFNQK'
'KIEEKVQFNDHNLAVKHFLNALKKNKIITELSEIGLIGHRVVQGANYFT'
'DAVLVDTHSLAKIKEFIKLAPLHNKPEADVIEIFLKEIKTAKNVAVFDT'
'TFHTTIPRENYLYAVPENXEKNNLVRRYGFHGTSYKYINEFLEKKFNKK'
'PLNLIVCHLGNGASVCAIKQGKSLNTSMGFTPLEGLIMGTRSGDIDPAI'
'VSYIAEQQKLSCNDVVNELNKKSGMFAITGSSDMRDIFDKPEINDIAIK'
'MYVNRVADYIAKYLNQLSGEIDSLVFTGGVGENASYCVQLIIEKVASLG'
'FKTNSNLFGNYQDSSLISTNESKYQIFRVRTNEELMIVEDALRVSTNIK'
'K',
'ILVVNAGSSSIKFQLFNDKKQVLAKGLCERIFIDGFFKLEFNQKKIEEK'
'VQFNDHNLAVKHFLNALKKNKIITELSEIGLIGHRVVQGANYFTDAVLV'
'DTHSLAKIKEFIKLAPLHNKPEADVIEIFLKEIKTAKNVAVFDTTFHTT'
'IPRENYLYAVPENXEKNNLVRRYGFHGTSYKYINEFLEKKFNKKPLNLI'
'VCHLGNGASVCAIKQGKSLNTSMGFTPLEGLIMGTRSGDIDPAIVSYIA'
'EQQKLSCNDVVNELNKKSGMFAITGSSDMRDIFDKPEINDIAIKMYVNR'
'VADYIAKYLNQLSGEIDSLVFTGGVGENASYCVQLIIEKVASLGFKTNS'
'NLFGNYQDSSLISTNESKYQIFRVRTNEELMIVEDALRV',
'ILVVNAGSSSIKFQLFNDKKQVLAKGLCERIFIDGFFKLEFNQKKIEEK'
'VQFNDHNLAVKHFLNALKKNKIITELSEIGLIGHRVVQGANYFTDAVLV'
'DTHSLAKIKEFIKLAPLHNKPEADVIEIFLKEIKTAKNVAVFDTTFHTT'
'IPRENYLYAVPENXEKNNLVRRYGFHGTSYKYINEFLEKKFNKKPLNLI'
'VCHLGNGASVCAIKQGKSLNTSMGFTPLEGLIMGTRSGDIDPAIVSYIA'
'EQQKLSCNDVVNELNKKSGMFAITGSSDMRDIFDKPEINDIAIKMYVNR'
'VADYIAKYLNQLSGEIDSLVFTGGVGENASYCVQLIIEKVASLGFKTNS'
'NLFGNYQDSSLISTNESKYQIFRVRTNEELMI']
})
def setUp(self):
self.tmp_dir = mkdtemp()
cases = ['WP_009885814.fna', 'WP_009885814.faa']
Test = namedtuple('Test', ['input', 'exp', 'obs'])
self.sam_tests = [Test(_get_named_data_path('%s.sam' % i),
_get_named_data_path('%s.txt' % i),
join(self.tmp_dir, '%s.txt' % i))
for i in cases]
self.filter_tests = [Test(_get_named_data_path('%s.diamond' % i),
_get_named_data_path('%s.best' % i),
join(self.tmp_dir, '%s.best'))
for i in cases]
self.filter_tests2 = [Test(_get_named_data_path('%s.sam' % i),
_get_named_data_path('%s.idcov' % i),
join(self.tmp_dir, '%s.idcov'))
for i in cases]
def setUp(self):
self.tmp_dir = mkdtemp()
cases = ['WP_009885814.fna', 'WP_009885814.faa']
Test = namedtuple('Test', ['input', 'exp', 'obs'])
self.sam_tests = [
Test(_get_named_data_path('%s.sam' % i),
_get_named_data_path('%s.txt' % i),
join(self.tmp_dir, '%s.txt' % i)) for i in cases
]
self.filter_tests = [
Test(_get_named_data_path('%s.diamond' % i),
_get_named_data_path('%s.best' % i),
join(self.tmp_dir, '%s.best')) for i in cases
]
self.filter_tests2 = [
Test(_get_named_data_path('%s.sam' % i),
_get_named_data_path('%s.idcov' % i),
join(self.tmp_dir, '%s.idcov')) for i in cases
]
def setUp(self):
self.tmp_dir = mkdtemp()
self.db_fa = _get_named_data_path("db.faa")
self.db = _get_named_data_path("db.dmnd")
self.neg_fp = [get_data_path(i) for i in ["empty", "whitespace_only"]]
def setUp(self):
self.tmp_dir = mkdtemp()
self.hmm_fp = _get_named_data_path('Pfam_B_1.hmm')
self.negative_fps = [get_data_path(i)
for i in ['empty', 'whitespace_only']]
def setUp(self):
super().setUp()
tests = [("blastp", "WP_009885814.faa"), ("blastx", "WP_009885814.fna")]
self.blast = [(i[0], get_data_path(i[1]), _get_named_data_path("%s.diamond" % i[1])) for i in tests]
def setUp(self):
self.tmp_dir = mkdtemp()
self.positive_fps = [
_get_named_data_path(i) for i in [
# modified from NC_018498.gbk
'NC_018498_partial_1.gbk',
'NC_018498_partial_1.gbk',
'NC_018498_partial_2.gbk',
]
]
self.positive_params = [{
'-p': 'meta'
}, {
'-p': 'meta',
'-f': 'gff'
}, {
'-p': 'single'
}]
self.positive_suffices = [{
'-o': 'gbk',
'-a': 'faa',
'-d': 'fna'
}, {
'-o': 'gff',
'-a': 'faa',
'-d': 'fna'
}, {
'-o': 'gbk',
'-a': 'faa',
'-d': 'fna'
}]
self.positive_outdir = ['test_1', 'test_2', 'test_3']
self.negative_fps = [
get_data_path(i) for i in ['empty', 'whitespace_only']
]
self.parse_fp = _get_named_data_path('parse_test.faa')
self.parse_exp = [{
Feature(type_='CDS',
id='1_1',
right_partial_=False,
left_partial_=False,
location='686..1828',
translation='MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNEYFSVKCNLNKYFLITSKSEPELKQILVPSR*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.236"',
rc_=False): [(685, 1828)],
Feature(type_='CDS',
id='1_2',
location='1828..>2757',
translation='MNLYDLLELPTTASIKEIKIAYKRLAKRYHPDVNKLGSQTFVEINNAYSILSDPNQKEKYFNYKTQHFID',
right_partial_=True,
left_partial_=False,
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.271"',
rc_=False): [(1827, 2757)]
}, {
Feature(type_='CDS',
id='2_1',
location='21577..22128',
right_partial_=False,
left_partial_=False,
translation='MKKTSPFILRRTKNKVLKELPKKIITDIYVELSEEHQKLYDKQKTDGLKEIKESDAKNALFDV*',
note='"start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.272"',
rc_=False): [(21576, 22128)]
}]
def setUp(self):
self.tmp_dir = mkdtemp()
self.db_fa = _get_named_data_path('db.faa')
self.db = _get_named_data_path('db.dmnd')
self.neg_fp = [get_data_path(i) for i in
['empty', 'whitespace_only']]
def setUp(self):
self.tmp_dir = mkdtemp()
self.db_fa = _get_named_data_path('db.faa')
self.db = _get_named_data_path('db.dmnd')
self.neg_fp = [get_data_path(i) for i in ['empty', 'whitespace_only']]
def test_run(self):
for case in self.cases:
run(self.tmp_dir, case.query, self.exp_db, aligner=case.aligner, tmpdir=self.tmp_dir)
obs = join(self.tmp_dir, 'db.sam')
self.assertTrue(
cmp(obs, _get_named_data_path(case.exp.sam), shallow=False))
