def setUp(self):
self.methods = ('pearson', 'spearman')
self.alternatives = ('two-sided', 'greater', 'less')
# Small dataset of minimal size (3x3). Mix of floats and ints in a
# native Python nested list structure.
self.minx = [[0, 1, 2], [1, 0, 3], [2, 3, 0]]
self.miny = [[0, 2, 7], [2, 0, 6], [7, 6, 0]]
self.minz = [[0, 0.5, 0.25], [0.5, 0, 0.1], [0.25, 0.1, 0]]
# No variation in distances. Taken from Figure 10.20(b), pg. 603 in L&L
# 3rd edition. Their example is 4x4 but using 3x3 here for easy
# comparison to the minimal dataset above.
self.no_variation = [[0, 0.667, 0.667],
[0.667, 0, 0.667],
[0.667, 0.667, 0]]
# This second dataset is derived from vegan::mantel's example dataset.
# The "veg" distance matrix contains Bray-Curtis distances derived from
# the varespec data (named "veg.dist" in the example). The "env"
# distance matrix contains Euclidean distances derived from scaled
# varechem data (named "env.dist" in the example).
self.veg_dm_vegan = np.loadtxt(
get_data_path('mantel_veg_dm_vegan.txt'))
self.env_dm_vegan = np.loadtxt(
get_data_path('mantel_env_dm_vegan.txt'))
# Expected test statistic when comparing x and y with method='pearson'.
self.exp_x_vs_y = 0.7559289
# Expected test statistic when comparing x and z with method='pearson'.
self.exp_x_vs_z = -0.9897433
def setUp(self):
self.multi_fp = get_data_path('ecoli_multi.sam')
self.single_fp = get_data_path('ecoli_single.sam')
self.single_exp = \
('MANLSGYNFAYLDEQTKRMIRRAILKAVAIPGYQVPFGGREMP'
'MPYGWGTGGIQLTASVIGESDVLKVIDQGADDTTNAVSIRNFF'
'KRVTGVNTTERTDDATLIQTRHRIPETPLTEDQIIIFQVPIPE'
'PLRFIEPRETETRTMHALEEYGVMQVKLYEDIARFGHIATTYA'
'YPVKVNGRYVMDPSPIPKFDNPKMDMMPALQLFGAGREKRIYA'
'VPPFTHVESLDFDDHPFTVQQWDEPCAICGSTHSYLDEVVLDD'
'AGNRMFVCSDTDYCRQQNEAKSQ', {
'@HD': 'VN:1.5\tSO:query',
'@PG': 'PN:DIAMOND',
'@mm': 'BlastX',
'QNAME': 'WP_000002278.1',
'FLAG': 0,
'RNAME': 'UniRef100_P16688',
'POS': 1,
'MAPQ': 255,
'CIGAR': '281M',
'RNEXT': '*',
'PNEXT': 0,
'TLEN': 0,
'QUAL': '*',
'AS': 573,
'NM': 3,
'ZR': 1477,
'ZE': 5.9e-164,
'ZI': 98,
'ZL': 281,
'ZF': 1,
'ZS': 1,
'MD': '102V117R54S5'
})
self.header_fp = get_data_path('header.sam')
def setUp(self):
# Crawford dataset for unweighted UniFrac
fp = get_data_path('PCoA_sample_data_3')
self.ordination = pcoa(DistanceMatrix.read(fp))
fp = get_data_path('PCoA_biplot_descriptors')
self.descriptors = pd.read_table(fp, index_col='Taxon').T
def test_default_valid_multi_line(self):
fp = get_data_path('blast7_default_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject2', 70.00, 5.0, 0.0, 0.0, 7.0,
60.0, 3.0, 100.0, 9e-05, 10.5],
['query1', 'subject2', 30.00, 8.0, 0.0, 0.0, 6.0,
15.0, 1.0, 100.0, 0.053, 12.0],
['query1', 'subject2', 90.00, 2.0, 0.0, 0.0, 9.0,
35.0, 2.0, 100.0, 0.002, 8.3]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
fp = get_data_path('legacy9_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject1', 90.00, 7.0, 1.0, 0.0, 0.0,
8.0, 4.0, 10.0, 1e-05, 15.5],
['query1', 'subject1', 70.00, 8.0, 0.0, 1.0, 0.0,
9.0, 5.0, 7.0, 0.231, 7.8],
['query1', 'subject1', 90.00, 5.0, 1.0, 1.0, 0.0,
0.0, 2.0, 10.0, 0.022, 13.0]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_any_sequences_to_fasta(self):
# test writing with default parameters
fh = io.StringIO()
_tabular_msa_to_fasta(self.msa, fh)
obs = fh.getvalue()
fh.close()
with io.open(get_data_path('fasta_3_seqs_defaults')) as fh:
exp = fh.read()
self.assertEqual(obs, exp)
# test writing with non-defaults
fasta_fh = io.StringIO()
qual_fh = io.StringIO()
_tabular_msa_to_fasta(self.msa, fasta_fh,
id_whitespace_replacement='*',
description_newline_replacement='+', max_width=3,
qual=qual_fh)
obs_fasta = fasta_fh.getvalue()
obs_qual = qual_fh.getvalue()
fasta_fh.close()
qual_fh.close()
with io.open(get_data_path('fasta_3_seqs_non_defaults')) as fh:
exp_fasta = fh.read()
with io.open(get_data_path('qual_3_seqs_non_defaults')) as fh:
exp_qual = fh.read()
self.assertEqual(obs_fasta, exp_fasta)
self.assertEqual(obs_qual, exp_qual)
def setUp(self):
"""varespec and varechem from Väre etal. 1995 DOI: 10.2307/3236351"""
self.Y = pd.read_csv(get_data_path('varespec.csv'), index_col=0)
self.X = pd.read_csv(get_data_path('varechem.csv'), index_col=0)
self.Y.index.name = None
self.X.index.name = None
def test_confirm_betadispr_results(self):
mp_dm = DistanceMatrix.read(get_data_path('moving_pictures_dm.tsv'))
mp_mf = pd.read_csv(get_data_path('moving_pictures_mf.tsv'), sep='\t')
mp_mf.set_index('#SampleID', inplace=True)
obs_med_mp = permdisp(mp_dm, mp_mf,
column='BodySite')
obs_cen_mp = permdisp(mp_dm, mp_mf, column='BodySite',
test='centroid')
exp_data_m = ['PERMDISP', 'F-value', 33, 4, 10.1956, 0.001, 999]
exp_data_c = ['PERMDISP', 'F-value', 33, 4, 17.4242, 0.001, 999]
exp_ind = ['method name', 'test statistic name', 'sample size',
'number of groups', 'test statistic', 'p-value',
'number of permutations']
exp_med_mp = pd.Series(data=exp_data_m, index=exp_ind, dtype='object',
name='PERMDISP results')
exp_cen_mp = pd.Series(data=exp_data_c, index=exp_ind, dtype='object',
name='PERMDISP results')
self.assert_series_equal(exp_med_mp, obs_med_mp)
self.assert_series_equal(exp_cen_mp, obs_cen_mp)
def setUp(self):
self.table1 = np.array(
[[1, 3, 0, 1, 0],
[0, 2, 0, 4, 4],
[0, 0, 6, 2, 1],
[0, 0, 1, 1, 1],
[5, 3, 5, 0, 0],
[0, 0, 0, 3, 5]])
self.sids1 = list('ABCDEF')
self.oids1 = ['OTU%d' % i for i in range(1, 6)]
self.t1 = TreeNode.read(
StringIO(u'(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
u'0.75,OTU5:0.75):1.25):0.0)root;'))
self.t1_w_extra_tips = TreeNode.read(
StringIO(u'(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
u'0.75,(OTU5:0.25,(OTU6:0.5,OTU7:0.5):0.5):0.5):1.25):0.0'
u')root;'))
self.t2 = TreeNode.read(
StringIO(u'((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)'
u'root;'))
self.oids2 = ['OTU%d' % i for i in range(1, 5)]
# the following table and tree are derived from the QIIME 1.9.1
# "tiny-test" data
tt_table_fp = get_data_path(
os.path.join('qiime-191-tt', 'otu-table.tsv'), 'data')
tt_tree_fp = get_data_path(
os.path.join('qiime-191-tt', 'tree.nwk'), 'data')
self.q_table = pd.read_csv(tt_table_fp, sep='\t', skiprows=1,
index_col=0)
self.q_tree = TreeNode.read(tt_tree_fp)
def setUp(self):
self.positives = [get_data_path(e) for e in [
'phylip_dna_3_seqs',
'phylip_single_seq_long',
'phylip_single_seq_short',
'phylip_two_chunks',
'phylip_variable_length_ids',
'phylip_varied_whitespace_in_seqs',
'phylip_whitespace_in_header_1',
'phylip_whitespace_in_header_2',
'phylip_whitespace_in_header_3',
]]
# negative tests for sniffer don't include
# phylip_invalid_empty_line_between_seqs, phylip_invalid_too_few_seqs,
# phylip_invalid_too_many_seqs - because sniffer only reads first seq
self.negatives = [get_data_path(e) for e in [
'empty',
'whitespace_only',
'phylip_invalid_empty_line_after_header',
'phylip_invalid_empty_line_before_header',
'phylip_invalid_header_too_long',
'phylip_invalid_header_too_short',
'phylip_invalid_no_header',
'phylip_invalid_seq_too_long',
'phylip_invalid_seq_too_short',
'phylip_invalid_zero_seq_len',
'phylip_invalid_zero_seqs',
]]
def setUp(self):
super(MantelTests, self).setUp()
self.methods = ('pearson', 'spearman')
self.alternatives = ('two-sided', 'greater', 'less')
# No variation in distances. Taken from Figure 10.20(b), pg. 603 in L&L
# 3rd edition. Their example is 4x4 but using 3x3 here for easy
# comparison to the minimal dataset above.
self.no_variation = [[0, 0.667, 0.667],
[0.667, 0, 0.667],
[0.667, 0.667, 0]]
# This second dataset is derived from vegan::mantel's example dataset.
# The "veg" distance matrix contains Bray-Curtis distances derived from
# the varespec data (named "veg.dist" in the example). The "env"
# distance matrix contains Euclidean distances derived from scaled
# varechem data (named "env.dist" in the example).
self.veg_dm_vegan = np.loadtxt(
get_data_path('mantel_veg_dm_vegan.txt'))
self.env_dm_vegan = np.loadtxt(
get_data_path('mantel_env_dm_vegan.txt'))
# Expected test statistic when comparing x and y with method='pearson'.
self.exp_x_vs_y = 0.7559289
# Expected test statistic when comparing x and z with method='pearson'.
self.exp_x_vs_z = -0.9897433
def test_any_sequences_to_fasta(self):
for fn, obj in ((_sequence_collection_to_fasta, self.seq_coll),
(_alignment_to_fasta, self.align)):
# test writing with default parameters
fh = StringIO()
fn(obj, fh)
obs = fh.getvalue()
fh.close()
with open(get_data_path('fasta_3_seqs_defaults'), 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
# test writing with non-defaults
fasta_fh = StringIO()
qual_fh = StringIO()
fn(obj, fasta_fh, id_whitespace_replacement='*',
description_newline_replacement='+', max_width=3, qual=qual_fh)
obs_fasta = fasta_fh.getvalue()
obs_qual = qual_fh.getvalue()
fasta_fh.close()
qual_fh.close()
with open(get_data_path('fasta_3_seqs_non_defaults'), 'U') as fh:
exp_fasta = fh.read()
with open(get_data_path('qual_3_seqs_non_defaults'), 'U') as fh:
exp_qual = fh.read()
self.assertEqual(obs_fasta, exp_fasta)
self.assertEqual(obs_qual, exp_qual)
def setUp(self):
self.jbe_con = get_data_path('test_contacts/1jbeA.psicov')
self.jbe_pdb = get_data_path('test_contacts/1jbeA_clean.pdb')
self.qjp_con = get_data_path('test_contacts/1qjpA.psicov')
self.qjp_pdb = get_data_path('test_contacts/1qjpA_clean.pdb')
self.real_n_con_qjp = {'lr': 6441,
'sr': 2337,
'all': 8778}
self.real_n_con_jbe = {'lr': 4742,
'sr': 2025,
'all': 6767}
self.positive_params = [
{'-t': 'all', '-l': 1},
{'-t': 'all', '-l': 2},
{'-t': 'all', '-l': 5},
{'-t': 'all', '-l': 10},
{'-t': 'lr', '-l': 1},
{'-t': 'lr', '-l': 2},
{'-t': 'lr', '-l': 10},
{'-t': 'sr', '-l': 2},
{'-t': 'sr', '-l': 10}]
def test_any_sequence_to_fasta(self):
# store writer function, sequence object to write, expected
# fasta filepath for default parameters, expected fasta filepath for
# non-defaults, and expected qual filepath for non-defaults
id_ = 'f o o'
desc = 'b\na\nr'
test_data = (
(_biological_sequence_to_fasta,
Sequence('ACGT', id=id_, description=desc,
quality=range(1, 5)),
('fasta_single_bio_seq_defaults',
'fasta_single_bio_seq_non_defaults',
'qual_single_bio_seq_non_defaults')),
(_dna_sequence_to_fasta,
DNA('TACG', id=id_, description=desc, quality=range(4)),
('fasta_single_dna_seq_defaults',
'fasta_single_dna_seq_non_defaults',
'qual_single_dna_seq_non_defaults')),
(_rna_sequence_to_fasta,
RNA('UACG', id=id_, description=desc, quality=range(2, 6)),
('fasta_single_rna_seq_defaults',
'fasta_single_rna_seq_non_defaults',
'qual_single_rna_seq_non_defaults')),
(_protein_sequence_to_fasta,
Protein('PQQ', id=id_, description=desc, quality=[42, 41, 40]),
('fasta_single_prot_seq_defaults',
'fasta_single_prot_seq_non_defaults',
'qual_single_prot_seq_non_defaults')))
for fn, obj, fps in test_data:
defaults_fp, non_defaults_fasta_fp, non_defaults_qual_fp = fps
# test writing with default parameters
fh = StringIO()
fn(obj, fh)
obs = fh.getvalue()
fh.close()
with open(get_data_path(defaults_fp), 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
# test writing with non-defaults
fasta_fh = StringIO()
qual_fh = StringIO()
fn(obj, fasta_fh, id_whitespace_replacement='-',
description_newline_replacement='_', max_width=1, qual=qual_fh)
obs_fasta = fasta_fh.getvalue()
obs_qual = qual_fh.getvalue()
fasta_fh.close()
qual_fh.close()
with open(get_data_path(non_defaults_fasta_fp), 'U') as fh:
exp_fasta = fh.read()
with open(get_data_path(non_defaults_qual_fp), 'U') as fh:
exp_qual = fh.read()
self.assertEqual(obs_fasta, exp_fasta)
self.assertEqual(obs_qual, exp_qual)
def test_simple(self):
eigvals = [0.51236726, 0.30071909, 0.26791207, 0.20898868,
0.19169895, 0.16054235, 0.15017696, 0.12245775,
0.0]
proportion_explained = [0.2675738328, 0.157044696, 0.1399118638,
0.1091402725, 0.1001110485,
0.0838401162, 0.0784269939,
0.0639511764, 0.0]
sample_ids = ['PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354',
'PC.593', 'PC.355', 'PC.607', 'PC.634']
axis_labels = ['PC%d' % i for i in range(1, 10)]
expected_results = OrdinationResults(
short_method_name='PCoA',
long_method_name='Principal Coordinate Analysis',
eigvals=pd.Series(eigvals, index=axis_labels),
samples=pd.DataFrame(
np.loadtxt(get_data_path('exp_PCoAEigenResults_site')),
index=sample_ids, columns=axis_labels),
proportion_explained=pd.Series(proportion_explained,
index=axis_labels))
dm = DistanceMatrix.read(get_data_path('PCoA_sample_data_3'))
results = pcoa(dm)
assert_ordination_results_equal(results, expected_results,
ignore_directionality=True)
def setUp(self):
self.positives = [get_data_path(e) for e in [
'fastq_multi_seq_sanger',
'fastq_single_seq_illumina1.3',
'fastq_wrapping_as_illumina_no_description',
'fastq_wrapping_as_sanger_no_description',
'fastq_wrapping_original_sanger_no_description',
'fastq_writer_illumina1.3_defaults',
'fastq_writer_sanger_defaults',
'fastq_writer_sanger_non_defaults',
'illumina_full_range_as_illumina.fastq',
'illumina_full_range_as_sanger.fastq',
'illumina_full_range_original_illumina.fastq',
'longreads_as_illumina.fastq',
'longreads_as_sanger.fastq',
'longreads_original_sanger.fastq',
'misc_dna_as_illumina.fastq',
'misc_dna_as_sanger.fastq',
'misc_dna_original_sanger.fastq',
'misc_rna_as_illumina.fastq',
'misc_rna_as_sanger.fastq',
'misc_rna_original_sanger.fastq',
'sanger_full_range_as_illumina.fastq',
'sanger_full_range_as_sanger.fastq',
'sanger_full_range_original_sanger.fastq',
'solexa_full_range_original_solexa.fastq',
'wrapping_as_illumina.fastq',
'wrapping_as_sanger.fastq',
'wrapping_original_sanger.fastq'
]]
self.negatives = [get_data_path(e) for e in [
'empty',
'whitespace_only',
'fastq_invalid_missing_header',
'fastq_invalid_missing_seq_data',
'error_diff_ids.fastq',
'error_double_qual.fastq',
'error_double_seq.fastq',
'error_long_qual.fastq',
'error_no_qual.fastq',
'error_qual_del.fastq',
'error_qual_escape.fastq',
'error_qual_null.fastq',
'error_qual_space.fastq',
'error_qual_tab.fastq',
'error_qual_unit_sep.fastq',
'error_qual_vtab.fastq',
'error_short_qual.fastq',
'error_spaces.fastq',
'error_tabs.fastq',
'error_trunc_at_seq.fastq',
'error_trunc_at_plus.fastq',
'error_trunc_at_qual.fastq',
'error_trunc_in_title.fastq',
'error_trunc_in_seq.fastq',
'error_trunc_in_plus.fastq',
'error_trunc_in_qual.fastq',
]]
def setUp(self):
self.cfg_fps = list()
self.misc_fp = get_data_path("misc.cfg")
self.misc_fp_local = get_data_path("misc_local.cfg")
self.param_fp = get_data_path("param.cfg")
self.param_fp_local = get_data_path("param_local.cfg")
self.patcher = mock.patch("click.get_app_dir", return_value=dirname(self.misc_fp))
self.patcher.start()
def test_filepaths_as_input(self):
dms = [
get_data_path('dm.txt'),
get_data_path('dm2.txt'),
]
np.random.seed(0)
obs = pwmantel(dms)
assert_data_frame_almost_equal(obs, self.exp_results_dm_dm2)
def test_phylogenetic_basis_large1(self):
fname = get_data_path('large_tree.nwk',
subfolder='data/phylogeny')
t = TreeNode.read(fname)
exp_basis = np.loadtxt(
get_data_path('large_tree_basis.txt',
subfolder='data/phylogeny'))
res_basis, res_keys = phylogenetic_basis(t)
npt.assert_allclose(exp_basis, res_basis)
def test_wrong_amount_of_columns_error(self):
fp = get_data_path("blast7_invalid_too_many_columns")
with assertRaisesRegex(self, BLAST7FormatError,
"Number of fields.*\(2\)"):
_blast7_to_data_frame(fp)
fp = get_data_path("legacy9_invalid_too_many_columns")
with assertRaisesRegex(self, BLAST7FormatError,
"Number of fields.*\(12\)"):
_blast7_to_data_frame(fp)
def setUp(self):
self.file_hhsearch1 = get_data_path(
'test_split_search/GRAMNEG_T1D_5168.out')
self.file_fasta1 = get_data_path(
'test_split_search/GRAMNEG_T1D_5168.fasta')
self.file_hhsearch2 = get_data_path(
'test_split_search/GRAMNEG_T1D_3144_1-275.out')
self.file_fasta2 = get_data_path(
'test_split_search/GRAMNEG_T1D_3144_1-275.fasta')
def test_scaling2(self):
scores = self.ordination.scores(2)
# Load data as computed with vegan 2.0-8
vegan_species = np.loadtxt(get_data_path("example2_species_scaling2_from_vegan"))
npt.assert_almost_equal(scores.species, vegan_species, decimal=6)
vegan_site = np.loadtxt(get_data_path("example2_site_scaling2_from_vegan"))
npt.assert_almost_equal(scores.site, vegan_site, decimal=6)
def setup(self):
"""Data from table 11.3 in Legendre & Legendre 1998."""
Y = np.loadtxt(get_data_path('example2_Y'))
X = np.loadtxt(get_data_path('example2_X'))
self.ordination = RDA(Y, X,
['Site0', 'Site1', 'Site2', 'Site3', 'Site4',
'Site5', 'Site6', 'Site7', 'Site8', 'Site9'],
['Species0', 'Species1', 'Species2', 'Species3',
'Species4', 'Species5'])
def setUp(self):
self.positives = [get_data_path(e) for e in [
'stockholm_extensive',
'stockholm_minimal',
'stockholm_rna',
'stockholm_runon_gf_with_whitespace',
'stockholm_runon_gf_no_whitespace',
'stockholm_duplicate_sequence_names',
'stockholm_duplicate_gr',
'stockholm_duplicate_gc',
'stockholm_invalid_nonexistent_gr',
'stockholm_invalid_nonexistent_gs',
'stockholm_no_data',
'stockholm_blank_lines',
'stockholm_differing_gc_data_length',
'stockholm_differing_gr_data_length',
'stockholm_differing_seq_lengths',
'stockholm_duplicate_sequence_names',
'stockholm_duplicate_tree_ids',
'stockholm_extensive_mixed',
'stockholm_invalid_data_type',
'stockholm_malformed_gf_line',
'stockholm_malformed_gs_line',
'stockholm_malformed_gr_line',
'stockholm_malformed_gc_line',
'stockholm_malformed_data_line',
'stockholm_metadata_only',
'stockholm_multiple_msa',
'stockholm_multiple_trees',
'stockholm_runon_gs_with_whitespace',
'stockholm_runon_gs_no_whitespace',
'stockholm_single_tree_with_id',
'stockholm_single_tree_without_id',
'stockholm_whitespace_only_lines',
'stockholm_all_data_types',
'stockholm_two_of_each_metadata',
'stockholm_data_only',
'stockholm_nonstring_labels',
'stockholm_missing_reference_items',
'stockholm_multiple_references',
'stockholm_runon_references',
'stockholm_runon_references_mixed',
'stockholm_single_reference',
'stockholm_missing_reference_items',
'stockholm_missing_rn_tag',
'stockholm_different_padding',
'stockholm_multi_line_tree_no_id',
'stockholm_multi_line_tree_with_id',
'stockholm_multiple_multi_line_trees'
]]
self.negatives = [get_data_path(e) for e in [
'stockholm_missing_header',
'empty',
'whitespace_only'
]]
def setup(self):
"""Data from table 11.3 in Legendre & Legendre 1998."""
Y = np.loadtxt(get_data_path("example2_Y"))
X = np.loadtxt(get_data_path("example2_X"))
self.ordination = RDA(
Y,
X,
["Site0", "Site1", "Site2", "Site3", "Site4", "Site5", "Site6", "Site7", "Site8", "Site9"],
["Species0", "Species1", "Species2", "Species3", "Species4", "Species5"],
)
def test_stockholm_runon_gs(self):
fp = get_data_path('stockholm_runon_gs_no_whitespace')
msa = _stockholm_to_tabular_msa(fp, constructor=DNA)
exp = TabularMSA([DNA('ATCGTTCAGTG',
metadata={'LN': 'This is a runon GS line.'})],
index=['seq1'])
self.assertEqual(msa, exp)
fp = get_data_path('stockholm_runon_gs_with_whitespace')
msa = _stockholm_to_tabular_msa(fp, constructor=DNA)
self.assertEqual(msa, exp)
def test_from_file_error(self):
for test_path in self.fferror_test_paths:
with open(get_data_path(test_path), 'U') as f:
with npt.assert_raises(FileFormatError):
OrdinationResults.from_file(f)
for test_path in self.verror_test_paths:
with open(get_data_path(test_path), 'U') as f:
with npt.assert_raises(ValueError):
OrdinationResults.from_file(f)
def test_balance_basis_large1(self):
fname = get_data_path('large_tree.nwk',
subfolder='data')
t = TreeNode.read(fname)
# note that the basis is in reverse level order
exp_basis = np.loadtxt(
get_data_path('large_tree_basis.txt',
subfolder='data'))
res_basis, res_keys = balance_basis(t)
npt.assert_allclose(exp_basis[:, ::-1], res_basis)
def test_create_config_overwrite(self):
cfg_obs = _create_config()
cfg_obs.read(get_data_path('default.cfg'))
# overwrite "db_path"
cfg_obs.read(get_data_path('param.cfg'))
cfg_exp = ConfigParser()
cfg_exp['DEFAULT']['db_path'] = 'db'
cfg_exp.add_section('prodigal')
cfg_exp['prodigal']['-t'] = '1'
self.assertEqual(cfg_obs, cfg_exp)
def test_scaling1(self):
scores = rda(self.Y, self.X, scaling=1)
sample_constraints = pd.DataFrame(np.loadtxt(
get_data_path('example2_sample_constraints_scaling1')))
# Load data as computed with vegan 2.0-8
vegan_features = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_species_scaling1_from_vegan')),
index=self.feature_ids,
columns=self.pc_ids)
vegan_samples = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_site_scaling1_from_vegan')),
index=self.sample_ids,
columns=self.pc_ids)
sample_constraints = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_sample_constraints_scaling1')),
index=self.sample_ids,
columns=self.pc_ids)
mat = np.loadtxt(get_data_path(
'example2_biplot_scaling1'))
cropped_pc_ids = self.pc_ids[:mat.shape[1]]
biplot_scores = pd.DataFrame(mat,
index=self.env_ids,
columns=cropped_pc_ids)
proportion_explained = pd.Series([0.44275783, 0.25614586,
0.15280354, 0.10497021,
0.02873375, 0.00987052,
0.00471828],
index=self.pc_ids)
eigvals = pd.Series([25.897954, 14.982578, 8.937841, 6.139956,
1.680705, 0.577350, 0.275984],
index=self.pc_ids)
exp = OrdinationResults(
'RDA', 'Redundancy Analysis',
samples=vegan_samples,
features=vegan_features,
sample_constraints=sample_constraints,
biplot_scores=biplot_scores,
proportion_explained=proportion_explained,
eigvals=eigvals)
assert_ordination_results_equal(scores, exp,
ignore_directionality=True,
decimal=6)
def setup(self):
"""Data from table 11.3 in Legendre & Legendre 1998
(p. 590). Loaded results as computed with vegan 2.0-8 and
compared with table 11.5 if also there."""
Y = np.loadtxt(get_data_path('example3_Y'))
X = np.loadtxt(get_data_path('example3_X'))
self.ordination = CCA(Y, X[:, :-1],
['Site0', 'Site1', 'Site2', 'Site3', 'Site4',
'Site5', 'Site6', 'Site7', 'Site8', 'Site9'],
['Species0', 'Species1', 'Species2', 'Species3',
'Species4', 'Species5', 'Species6', 'Species7',
'Species8'])
def test_stockholm_mixed_runon_references(self):
fp = get_data_path('stockholm_runon_references_mixed')
msa = _stockholm_to_tabular_msa(fp, constructor=DNA)
exp = TabularMSA(
[],
metadata={
'RN': [
OrderedDict([('RC', 'A Runon Comment'),
('RM', '123456789'), ('RT', 'A Runon Title'),
('RA', 'The Author'), ('RL', 'A Location')])
]
})
self.assertEqual(msa, exp)
def setUp(self):
self.jbe_con = get_data_path('1jbeA.psicov')
self.jbe_pdb = get_data_path('1jbeA_clean.pdb')
self.qjp_con = get_data_path('1qjpA.psicov')
self.qjp_pdb = get_data_path('1qjpA_clean.pdb')
self.real_n_con_qjp = {'lr': 6441, 'sr': 2337, 'all': 8778}
self.real_n_con_jbe = {'lr': 4742, 'sr': 2025, 'all': 6767}
self.positive_params = [{
'-t': 'all',
'-l': 1
}, {
'-t': 'all',
'-l': 2
}, {
'-t': 'all',
'-l': 5
}, {
'-t': 'all',
'-l': 10
}, {
'-t': 'lr',
'-l': 1
}, {
'-t': 'lr',
'-l': 2
}, {
'-t': 'lr',
'-l': 10
}, {
'-t': 'sr',
'-l': 2
}, {
'-t': 'sr',
'-l': 10
}]
def test_from_seralized_results(self):
# the current implementation of ordination results loses some
# information, test that pcoa_biplot works fine regardless
results = OrdinationResults.read(get_data_path('PCoA_skbio'))
serialized = pcoa_biplot(results, self.descriptors)
in_memory = pcoa_biplot(self.ordination, self.descriptors)
assert_ordination_results_equal(serialized,
in_memory,
ignore_directionality=True,
ignore_axis_labels=True,
ignore_method_names=True)
def setUp(self):
self.positives = [get_data_path(e) for e in [
'blast7_default_single_line',
'blast7_default_multi_line',
'blast7_custom_minimal',
'blast7_custom_single_line',
'blast7_custom_multi_line',
'blast7_custom_mixed_nans',
'blast7_invalid_differing_fields',
'blast7_invalid_no_data',
'blast7_invalid_too_many_columns',
'legacy9_and_blast7_default',
'legacy9_invalid_too_many_columns',
'legacy9_mixed_nans',
'legacy9_multi_line',
'legacy9_single_line']]
self.negatives = [get_data_path(e) for e in [
'blast7_invalid_gibberish',
'blast7_invalid_for_sniffer',
'blast7_invalid_for_sniffer_2',
'empty']]
def test_custom_valid_multi_line(self):
fp = get_data_path("blast7_custom_multi_line")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[1.0, 8.0, 3.0, 10.0, 8.0, 0.0, 1.0, 'query1',
'subject2'],
[2.0, 5.0, 2.0, 15.0, 8.0, 0.0, 2.0, 'query1',
'subject2'],
[1.0, 6.0, 2.0, 12.0, 8.0, 0.0, 1.0, 'query1',
'subject2']],
columns=['qstart', 'qend', 'sstart', 'send',
'nident', 'mismatch', 'sframe',
'qaccver', 'saccver'])
assert_data_frame_almost_equal(df, exp)
def test__qiime2_rclr(self):
"""Tests q2-rclr matches standalone rclr."""
# make mock table to write
samps_ids = ['s%i' % i for i in range(self.cdata.shape[0])]
feats_ids = ['f%i' % i for i in range(self.cdata.shape[1])]
table_test = Table(self.cdata.T, feats_ids, samps_ids)
# write table
in_ = get_data_path('test.biom', subfolder='data')
out_path = os_path_sep.join(in_.split(os_path_sep)[:-1])
test_path = os.path.join(out_path, 'rclr-test.biom')
with biom_open(test_path, 'w') as wf:
table_test.to_hdf5(wf, "test")
# run standalone
runner = CliRunner()
result = runner.invoke(sdc.commands['rclr'],
['--in-biom', test_path,
'--output-dir', out_path])
out_table = get_data_path('rclr-table.biom',
subfolder='data')
res_table = load_table(out_table)
standalone_mat = res_table.matrix_data.toarray().T
# check that exit code was 0 (indicating success)
try:
self.assertEqual(0, result.exit_code)
except AssertionError:
ex = result.exception
error = Exception('Command failed with non-zero exit code')
raise error.with_traceback(ex.__traceback__)
# run QIIME2
q2_table_test = Artifact.import_data("FeatureTable[Frequency]",
table_test)
q2_res = rclr_transformation(q2_table_test).rclr_table.view(Table)
q2_res_mat = q2_res.matrix_data.toarray().T
# check same and check both correct
npt.assert_allclose(standalone_mat, q2_res_mat)
npt.assert_allclose(standalone_mat, self.true)
npt.assert_allclose(q2_res_mat, self.true)
def test_stockholm_to_msa_different_padding(self):
fp = get_data_path('stockholm_different_padding')
msa = _stockholm_to_tabular_msa(fp, constructor=DNA)
exp = TabularMSA(
[],
metadata={
'RN': [
OrderedDict([('RC', 'A Runon Comment Without '
'Whitespace')]),
OrderedDict([('RC', 'A Runon Comment With '
'Whitespace')])
]
})
self.assertEqual(msa, exp)
def test_proportional_artifact(self):
from qiime2.plugins.gneiss.methods import correlation_clustering
table_f = get_data_path("feature-table.qza")
in_table = qiime2.Artifact.load(table_f)
res = correlation_clustering(in_table, pseudocount=0.1)
res_clust = res.clustering._view(TreeNode)
exp_str = ('((F4:0.228723591874,(F5:0.074748541601,'
'(F1:0.00010428164962,F2:0.00010428164962)'
'y4:0.0746442599513)y3:0.153975050273)'
'y1:0.70266138894,(F3:0.266841737789,F6:0.266841737789)'
'y2:0.664543243026)y0;\n')
exp_tree = TreeNode.read([exp_str])
self.assert_tree_almost_equals(exp_tree, res_clust)
def test_assign_ids_intersect(self):
from qiime2.plugins.gneiss.methods import assign_ids
tree_f = get_data_path("tree_extra.qza")
table_f = get_data_path("polytomy_table.qza")
tree = qiime2.Artifact.load(tree_f)
table = qiime2.Artifact.load(table_f)
output = assign_ids(input_tree=tree, input_table=table)
res_tree = output.output_tree._view(TreeNode)
res_table = output.output_table._view(pd.DataFrame)
for n in res_tree.levelorder(include_self=True):
self.assertTrue(n.name is not None)
exp = list('abde')
res = [n.name for n in res_tree.tips()]
self.assertEqual(exp, res)
exp = pd.DataFrame(
{
's1': [1.0, 2.0, 4.0, 5.0],
's2': [1.0, 5.0, 6.0, 0.0]
},
index=['a', 'b', 'd', 'e']).T
pdt.assert_frame_equal(exp, res_table)
def test_valid_nan_handling(self):
fp = get_data_path('blast6_custom_mixed_nans')
df = _blast6_to_data_frame(fp,
columns=[
'qacc', 'qseq', 'btop', 'sframe',
'ppos', 'positive', 'gaps'
])
exp = pd.DataFrame(
[[np.nan, 'PAAWWWWW', 8.0, 1.0, 100.00, np.nan, 0.0],
['query1', np.nan, 8.0, 1.0, np.nan, 8.0, 0.0]],
columns=[
'qacc', 'qseq', 'btop', 'sframe', 'ppos', 'positive', 'gaps'
])
assert_data_frame_almost_equal(df, exp)
def test_getoptS_small(self):
"""Test singular values from U and V."""
data = loadmat(get_data_path('small_test.mat'))
M_E = np.array(data['M_E'].todense())
E = data['E']
x = data['x']
y = data['y']
res = singular_values(x, y, M_E, E)
exp = np.array([[0.93639499, 0.07644197, -0.02828782],
[-0.03960841, 0.60787383, 0.00521257],
[0.00729038, 0.00785834, 0.67853083]])
npt.assert_allclose(res, exp, atol=1e-5)
def test_getoptS_small(self):
# warning : this test must ALWAYS pass
data = loadmat(get_data_path('small_test.mat'))
M_E = np.array(data['M_E'].todense())
E = data['E']
x = data['x']
y = data['y']
res = getoptS(x, y, M_E, E)
exp = np.array([[0.93639499, 0.07644197, -0.02828782],
[-0.03960841, 0.60787383, 0.00521257],
[0.00729038, 0.00785834, 0.67853083]])
npt.assert_allclose(res, exp, atol=1e-5)
def setUp(self):
self.valid_files = [
([('f o o', 'bar\n\nbaz', 'AACCGG', [16, 17, 18, 19, 20, 21]),
('bar', 'baz foo', 'TTGGCC', [23, 22, 21, 20, 19, 18]),
('ba\n\t\tz', 'foo bar', 'GATTTC', [20, 21, 22, 23, 24, 18])],
[({
'variant': 'sanger'
}, get_data_path('fastq_writer_sanger_defaults')),
({
'phred_offset': 33
}, get_data_path('fastq_writer_sanger_defaults')),
({
'variant': 'illumina1.8'
}, get_data_path('fastq_writer_sanger_defaults')),
({
'variant': 'illumina1.3'
}, get_data_path('fastq_writer_illumina1.3_defaults')),
({
'variant': 'sanger',
'id_whitespace_replacement': '%',
'description_newline_replacement': '^'
}, get_data_path('fastq_writer_sanger_non_defaults'))]),
]
def test_no_collapsed_nodes(self):
st = TreeNode.read(get_data_path(self.newick))
tr, ts = diamondtree(st,
breadth_scaling=6,
depth_scaling=30,
cladecolors={
'y5': '#FF0000',
'y18': '#0000FF'
},
bgcolors={'y29': '#00FF00'})
tr.render(file_name=self.fname, tree_style=ts)
self.assertTrue(os.path.exists(self.fname))
self.assertTrue(os.path.getsize(self.fname) > 0)
def test_standalone_rclr(self):
"""Test the standalone rlcr."""
# make mock table to write
samps_ids = ['s%i' % i for i in range(self.cdata.shape[0])]
feats_ids = ['f%i' % i for i in range(self.cdata.shape[1])]
table_test = Table(self.cdata.T, feats_ids, samps_ids)
# write table
in_ = get_data_path('test.biom', subfolder='rpca_data')
out_path = os_path_sep.join(in_.split(os_path_sep)[:-1])
test_path = os.path.join(out_path, 'rclr-test.biom')
with biom_open(test_path, 'w') as wf:
table_test.to_hdf5(wf, "test")
runner = CliRunner()
result = runner.invoke(sdc.commands['rclr'],
['--in-biom', test_path,
'--output-dir', out_path])
out_table = get_data_path('rclr-table.biom',
subfolder='rpca_data')
res_table = load_table(out_table)
test_cmat = res_table.matrix_data.toarray().T
npt.assert_allclose(test_cmat, self.true)
# Lastly, check that exit code was 0 (indicating success)
CliTestCase().assertExitCode(0, result)
def test_fastq_to_generator_invalid_files_illumina(self):
# files that should be invalid for illumina1.3 and illumina1.8 variants
fps = [
get_data_path(fp) for fp in [
'sanger_full_range_original_sanger.fastq',
'solexa_full_range_original_solexa.fastq'
]
]
for fp in fps:
with self.assertRaisesRegexp(ValueError, 'out of range \[0, 62\]'):
list(_fastq_to_generator(fp, variant='illumina1.3'))
with self.assertRaisesRegexp(ValueError, 'out of range \[0, 62\]'):
list(_fastq_to_generator(fp, variant='illumina1.8'))
def setUp(self):
"""Data from table 11.3 in Legendre & Legendre 1998
(p. 590). Loaded results as computed with vegan 2.0-8 and
compared with table 11.5 if also there."""
self.feature_ids = [
'Feature0', 'Feature1', 'Feature2', 'Feature3', 'Feature4',
'Feature5', 'Feature6', 'Feature7', 'Feature8'
]
self.sample_ids = [
'Sample0', 'Sample1', 'Sample2', 'Sample3', 'Sample4', 'Sample5',
'Sample6', 'Sample7', 'Sample8', 'Sample9'
]
self.env_ids = ['Constraint0', 'Constraint1', 'Constraint2']
self.pc_ids = [
'CCA1', 'CCA2', 'CCA3', 'CCA4', 'CCA5', 'CCA6', 'CCA7', 'CCA8',
'CCA9'
]
self.Y = pd.DataFrame(np.loadtxt(get_data_path('example3_Y')),
columns=self.feature_ids,
index=self.sample_ids)
self.X = pd.DataFrame(np.loadtxt(get_data_path('example3_X'))[:, :-1],
columns=self.env_ids,
index=self.sample_ids)
def test_standalone_rpca(self):
"""Checks the output produced by gemelli's RPCA standalone script.
This is more of an "integration test" than a unit test -- the
details of the algorithm used by the standalone RPCA script are
checked in more detail in gemelli/tests/test_optspace.py, etc.
"""
in_ = get_data_path('test.biom', subfolder='rpca_data')
out_ = os_path_sep.join(in_.split(os_path_sep)[:-1])
runner = CliRunner()
result = runner.invoke(sdc.commands['rpca'],
['--in-biom', in_, '--output-dir', out_])
# Read the results
dist_res = pd.read_csv(get_data_path('distance-matrix.tsv',
subfolder='rpca_data'),
sep='\t',
index_col=0)
ord_res = OrdinationResults.read(
get_data_path('ordination.txt', subfolder='rpca_data'))
# Read the expected results
dist_exp = pd.read_csv(get_data_path('expected-distance-matrix.tsv',
subfolder='rpca_data'),
sep='\t',
index_col=0)
ord_exp = OrdinationResults.read(
get_data_path('expected-ordination.txt', subfolder='rpca_data'))
# Check that the distance matrix matches our expectations
assert_array_almost_equal(dist_res.values, dist_exp.values)
# Check that the ordination results match our expectations -- checking
# each value for both features and samples
assert_ordinationresults_equal(ord_res, ord_exp)
# Lastly, check that gemelli's exit code was 0 (indicating success)
CliTestCase().assertExitCode(0, result)
def test_scaling1(self):
scores = rda(self.Y, self.X, scaling=1)
biplot_scores = pd.DataFrame(np.loadtxt(
get_data_path('example2_biplot_scaling1')))
sample_constraints = pd.DataFrame(np.loadtxt(
get_data_path('example2_sample_constraints_scaling1')))
# Load data as computed with vegan 2.0-8
vegan_features = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_species_scaling1_from_vegan')),
index=self.feature_ids,
columns=self.pc_ids)
vegan_samples = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_site_scaling1_from_vegan')),
index=self.sample_ids,
columns=self.pc_ids)
sample_constraints = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_sample_constraints_scaling1')),
index=self.sample_ids,
columns=self.pc_ids)
biplot_scores = pd.DataFrame(
np.loadtxt(get_data_path(
'example2_biplot_scaling1')))
# These are wrong. See issue #1002
proportion_explained = pd.Series([0.44275783, 0.25614586,
0.15280354, 0.10497021,
0.02873375, 0.00987052,
0.00471828],
index=self.pc_ids)
# These are wrong. See issue #1002
eigvals = pd.Series([25.897954, 14.982578, 8.937841, 6.139956,
1.680705, 0.577350, 0.275984],
index=self.pc_ids)
exp = OrdinationResults(
'RDA', 'Redundancy Analysis',
samples=vegan_samples,
features=vegan_features,
sample_constraints=sample_constraints,
biplot_scores=biplot_scores,
proportion_explained=proportion_explained,
eigvals=eigvals)
assert_ordination_results_equal(scores, exp,
ignore_directionality=True,
ignore_biplot_scores_labels=True,
decimal=6)
def test_standalone_rpca_rank_est(self):
"""Checks the standalone rank estimate
is used instead of a explicit rank
setting.
"""
in_ = get_data_path('test.biom')
out_ = os_path_sep.join(in_.split(os_path_sep)[:-1])
runner = CliRunner()
result = runner.invoke(sdc.commands['auto-rpca'],
['--in-biom', in_,
'--output-dir', out_])
# Read the results
dist_res = pd.read_csv(get_data_path('distance-matrix.tsv'), sep='\t',
index_col=0)
ord_res = OrdinationResults.read(get_data_path('ordination.txt'))
# Read the expected results
file_ = 'expected-est-distance-matrix.tsv'
dist_exp = pd.read_csv(get_data_path(file_),
sep='\t', index_col=0)
ord_exp = OrdinationResults.read(get_data_path(
'expected-est-ordination.txt'))
# Check that the distance matrix matches our expectations
assert_array_almost_equal(dist_res.values, dist_exp.values)
# Check that the ordination results match our expectations -- checking
# each value for both features and samples
assert_deicode_ordinationresults_equal(ord_res, ord_exp)
# Lastly, check that DEICODE's exit code was 0 (indicating success)
try:
self.assertEqual(0, result.exit_code)
except AssertionError:
ex = result.exception
error = Exception('Command failed with non-zero exit code')
raise error.with_traceback(ex.__traceback__)
def test_msa_to_stockholm_data_only(self):
fp = get_data_path('stockholm_data_only')
msa = TabularMSA([
RNA('ACUCCGACAUGCUCC'),
RNA('UAGUGCCGAACGCUG'),
RNA('GUGUGGGCGUGAUUC')
],
index=['seq1', 'seq2', 'seq3'])
fh = io.StringIO()
_tabular_msa_to_stockholm(msa, fh)
obs = fh.getvalue()
fh.close()
with io.open(fp) as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_lme_artifact(self):
from qiime2.plugins.gneiss.visualizers import lme_regression
table_f = get_data_path("lme_balances.qza")
tree_f = get_data_path("lme_tree.qza")
metadata_f = get_data_path("test_lme_metadata.txt")
in_table = qiime2.Artifact.load(table_f)
in_tree = qiime2.Artifact.load(tree_f)
in_metadata = qiime2.Metadata(pd.read_table(metadata_f, index_col=0))
viz = lme_regression(in_table, in_tree, in_metadata, 'ph',
'host_subject_id')
os.mkdir('regression_summary_dir')
viz.visualization.export_data('regression_summary_dir')
res_coef = pd.read_csv(os.path.join('regression_summary_dir',
'coefficients.csv'),
index_col=0)
self.assertAlmostEqual(res_coef.loc['y0', 'groups RE'],
1.105630e+00,
places=5)
shutil.rmtree('regression_summary_dir')
def test_msa_to_stockholm_multiple_trees(self):
fp = get_data_path('stockholm_multiple_trees')
msa = TabularMSA([],
metadata=OrderedDict([('NH',
OrderedDict([('tree1', 'ABCD'),
('tree2', 'EFGH'),
('tree3', 'IJKL')
]))]))
fh = io.StringIO()
_tabular_msa_to_stockholm(msa, fh)
obs = fh.getvalue()
fh.close()
with io.open(fp) as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_parse_easel_output(self):
obs = parse_easel_output(self.fp_infernal)
self.assertEqual('INFERNAL', obs['software'].iloc[0])
self.assertEqual('1.1.2', obs['software version'].iloc[0])
self.assertEqual('Markergenes/FSSC/allFSSC.cm',
obs['fp_query'].iloc[0])
self.assertEqual('Sequences_Fusarium/taxid_99000016/FW16.genome.fna',
obs['fp_target'].iloc[0])
with open(get_data_path('easel2sam/exp_parse_easle_output.txt')) as f:
exp = ''.join(f.readlines())
assert_frame_equal(_str2pd(exp), obs)
obs = parse_easel_output(self.fp_nohit)
self.assertEqual(obs.shape[0], 0)
def test_standalone_rpca_rank_est(self):
"""Checks the standalone RPCA rank estimate
is used instead of a explicit rank
setting.
"""
in_ = get_data_path('test.biom', subfolder='rpca_data')
out_ = os_path_sep.join(in_.split(os_path_sep)[:-1])
runner = CliRunner()
result = runner.invoke(sdc.commands['auto-rpca'],
['--in-biom', in_, '--output-dir', out_])
# Read the results
dist_res = pd.read_csv(get_data_path('distance-matrix.tsv',
subfolder='rpca_data'),
sep='\t',
index_col=0)
ord_res = OrdinationResults.read(
get_data_path('ordination.txt', subfolder='rpca_data'))
# Read the expected results
file_ = 'expected-est-distance-matrix.tsv'
dist_exp = pd.read_csv(get_data_path(file_, subfolder='rpca_data'),
sep='\t',
index_col=0)
ord_exp = OrdinationResults.read(
get_data_path('expected-est-ordination.txt',
subfolder='rpca_data'))
# Check that the distance matrix matches our expectations
assert_array_almost_equal(dist_res.values, dist_exp.values)
# Check that the ordination results match our expectations -- checking
# each value for both features and samples
assert_ordinationresults_equal(ord_res, ord_exp)
# Lastly, check that gemelli's exit code was 0 (indicating success)
CliTestCase().assertExitCode(0, result)
def test_stockholm_maintains_order(self):
fp = get_data_path('stockholm_two_of_each_metadata')
msa = _stockholm_to_tabular_msa(fp, constructor=DNA)
msa_order = list(msa.metadata.items())
exp_order = [('NM', 'Kestrel Gorlick'), ('DT', 'February 5th, 2016')]
self.assertEqual(msa_order, exp_order)
msa_order = list(msa[0].metadata.items())
exp_order = [('AL', 'ABCD'), ('NS', '1234')]
self.assertEqual(msa_order, exp_order)
msa_order = list(msa.positional_metadata.columns)
exp_order = ['SS_cons', 'AS_cons']
self.assertEqual(msa_order, exp_order)
msa_order = list(msa[0].positional_metadata.columns)
exp_order = ['SS', 'AS']
self.assertEqual(msa_order, exp_order)
def test_pcoa_biplot_from_ape(self):
"""Test against a reference implementation from R's ape package
The test data was generated with the R script below and using a
modified version of pcoa.biplot that returns the U matrix.
library(ape)
# files can be found in the test data folder of the ordination module
y = t(read.table('PCoA_biplot_descriptors', row.names = 1, header = 1))
dm = read.table('PCoA_sample_data_3', row.names = 1, header = 1)
h = pcoa(dm)
# biplot.pcoa will only calculate the biplot for two axes at a time
acc = NULL
for (axes in c(1, 3, 5, 7)) {
new = biplot.pcoa(h, y, plot.axes=c(axes, axes+1),
rn = rep('.', length(colnames(dm))) )
if(is.null(acc)) {
acc = new
}
else {
b = acc
acc <- cbind(acc, new)
}
}
write.csv(acc, file='PCoA_biplot_projected_descriptors')
"""
obs = pcoa_biplot(self.ordination, self.descriptors)
# we'll build a dummy ordination results object based on the expected
# the main thing we'll compare and modify is the features dataframe
exp = deepcopy(obs)
fp = get_data_path('PCoA_biplot_projected_descriptors')
# R won't calculate the last dimension, so pad with zeros to make the
# arrays comparable
exp.features = pd.read_table(fp, sep=',', index_col=0)
exp.features['Axis.9'] = np.zeros_like(exp.features['Axis.8'])
# make the order comparable
exp.features = exp.features.reindex(obs.features.index)
assert_ordination_results_equal(obs,
exp,
ignore_directionality=True,
ignore_axis_labels=True)
def test_parse(self):
imd1 = IntervalMetadata(None)
imd1.add(bounds=[(3588441, 3588818)],
metadata={
'ncRNA_class': 'RNaseP_bact_a',
'type': 'ncRNA',
'strand': '-',
'db_xref': 'RF00010',
'source': 'Rfam'
})
imd1.add(bounds=[(3355449, 3355633)],
metadata={
'ncRNA_class': '5S_rRNA',
'type': 'rRNA',
'strand': '+',
'product': '5s_rRNA',
'db_xref': 'RF00001',
'source': 'Rfam'
})
imd2 = IntervalMetadata(None)
imd2.add(bounds=[(85215, 85384)],
metadata={
'ncRNA_class': 'LSU_rRNA_bacteria',
'type': 'rRNA',
'strand': '+',
'product': '23s_rRNA',
'db_xref': 'RF02541',
'source': 'Rfam'
})
imd3 = IntervalMetadata(None)
imd3.add(bounds=[(8739, 8777)],
metadata={
'ncRNA_class': 'SSU_rRNA_bacteria',
'type': 'rRNA',
'strand': '+',
'product': '16s_rRNA',
'db_xref': 'RF00177',
'source': 'Rfam'
})
exp = (('NC_016822.1', imd1), ('NC_016833.1', imd2), ('NC_016834.1',
imd3))
fp = get_data_path('cmscan.txt')
gen = _generator(fp)
for (exp_id, exp_imd), (obs_id, obs_imd) in zip(exp, gen):
self.assertEqual(exp_id, obs_id)
self.assertEqual(exp_imd, obs_imd)
def test_standalone_rpca(self):
"""Checks the output produced by gemelli's standalone script.
This is more of an "integration test" than a unit test -- the
details of the algorithm used by the standalone CTF script are
checked in more detail in gemelli/tests/test_factorization.py.
"""
in_table = get_data_path('test-small.biom')
in_meta = get_data_path('test-small.tsv')
out_ = os_path_sep.join(in_table.split(os_path_sep)[:-1])
runner = CliRunner()
result = runner.invoke(standalone_ctf,
['--in-biom',
in_table,
'--sample-metadata-file',
in_meta,
'--individual-id-column',
'host_subject_id',
'--state-column-1',
'context',
'--output-dir',
out_])
# check exit code was 0 (indicating success)
CliTestCase().assertExitCode(0, result)
# Read the results
samp_res = pd.read_csv(
get_data_path('context-subject-ordination.tsv'),
sep='\t',
index_col=0)
feat_res = pd.read_csv(
get_data_path('context-features-ordination.tsv'),
sep='\t',
index_col=0)
# Read the expected results
samp_exp = pd.read_csv(
get_data_path('expected-context-subject-ordination.tsv'),
sep='\t',
index_col=0)
feat_exp = pd.read_csv(
get_data_path('expected-context-features-ordination.tsv'),
sep='\t',
index_col=0)
# Check that the distance matrix matches our expectations
comp_col = ['PC1', 'PC2', 'PC3']
cent_ = samp_res[comp_col].mean().values.max()
self.assertAlmostEqual(cent_, 0)
cent_ = feat_res[comp_col].mean().values.max()
self.assertAlmostEqual(cent_, 0)
# check matched
assert_allclose(absolute_sort(samp_res[comp_col].values),
absolute_sort(samp_exp[comp_col].values),
atol=.5)
assert_allclose(absolute_sort(feat_res[comp_col].values),
absolute_sort(feat_exp[comp_col].values),
atol=.5)
def test_msa_to_stockholm_nonstring_values(self):
fp = get_data_path('stockholm_nonstring_labels')
msa = TabularMSA([DNA('ACTG', metadata=OrderedDict([(8, 123)]),
positional_metadata=OrderedDict([(1.0,
[1, 2, 3, 4])])
)],
metadata=OrderedDict([(1.3, 2857)]),
positional_metadata=OrderedDict([(25, [4, 3, 2, 1])]),
index=[11214])
fh = io.StringIO()
_tabular_msa_to_stockholm(msa, fh)
obs = fh.getvalue()
fh.close()
with io.open(fp) as fh:
exp = fh.read()
self.assertEqual(obs, exp)
