def calculate_tetra(infiles):
"""Calculate TETRA for files in input directory.
- infiles - paths to each input file
- org_lengths - dictionary of input sequence lengths, keyed by sequence
Calculates TETRA correlation scores, as described in:
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for
the prokaryotic species definition. Proc Natl Acad Sci USA 106:
19126-19131. doi:10.1073/pnas.0906412106.
and
Teeling et al. (2004) Application of tetranucleotide frequencies for the
assignment of genomic fragments. Env. Microbiol. 6(9): 938-947.
doi:10.1111/j.1462-2920.2004.00624.x
"""
logger.info("Running TETRA.")
# First, find Z-scores
logger.info("Calculating TETRA Z-scores for each sequence.")
tetra_zscores = {}
for filename in infiles:
logger.info("Calculating TETRA Z-scores for %s", filename)
org = os.path.splitext(os.path.split(filename)[-1])[0]
tetra_zscores[org] = tetra.calculate_tetra_zscore(filename)
# Then calculate Pearson correlation between Z-scores for each sequence
logger.info("Calculating TETRA correlation scores.")
tetra_correlations = tetra.calculate_correlations(tetra_zscores)
return (tetra_correlations, )
def calculate_tetra(infiles: List[Path]) -> pd.DataFrame:
"""Calculate TETRA for files in input directory.
:param logger: logging object
:param infiles: list, paths to each input file
Calculates TETRA correlation scores, as described in:
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for
the prokaryotic species definition. Proc Natl Acad Sci USA 106:
19126-19131. doi:10.1073/pnas.0906412106.
and
Teeling et al. (2004) Application of tetranucleotide frequencies for the
assignment of genomic fragments. Env. Microbiol. 6(9): 938-947.
doi:10.1111/j.1462-2920.2004.00624.x
"""
logger = logging.getLogger(__name__)
logger.info("Running TETRA.")
# First, find Z-scores
logger.info("Calculating TETRA Z-scores for each sequence.")
tetra_zscores = {}
for filename in infiles:
logger.info("Calculating TETRA Z-scores for %s", filename)
tetra_zscores[filename.stem] = tetra.calculate_tetra_zscore(filename)
# Then calculate Pearson correlation between Z-scores for each sequence
logger.info("Calculating TETRA correlation scores.")
tetra_correlations = tetra.calculate_correlations(tetra_zscores)
return tetra_correlations
def calculate_tetra(infiles, org_lengths):
"""Calculate TETRA for files in input directory.
- infiles - paths to each input file
- org_lengths - dictionary of input sequence lengths, keyed by sequence
Calculates TETRA correlation scores, as described in:
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the
prokaryotic species definition. Proc Natl Acad Sci USA 106: 19126-19131.
doi:10.1073/pnas.0906412106.
and
Teeling et al. (2004) Application of tetranucleotide frequencies for the
assignment of genomic fragments. Env. Microbiol. 6(9): 938-947.
doi:10.1111/j.1462-2920.2004.00624.x
"""
logger.info("Running TETRA.")
# First, find Z-scores
logger.info("Calculating TETRA Z-scores for each sequence.")
tetra_zscores = {}
for filename in infiles:
logger.info("Calculating TETRA Z-scores for %s" % filename)
org = os.path.splitext(os.path.split(filename)[-1])[0]
tetra_zscores[org] = tetra.calculate_tetra_zscore(filename)
# Then calculate Pearson correlation between Z-scores for each sequence
logger.info("Calculating TETRA correlation scores.")
tetra_correlations = tetra.calculate_correlations(tetra_zscores)
return (tetra_correlations, )
def test_tetra_concordance(
paths_concordance_fna, path_concordance_jspecies, tolerance_tetra, tmp_path
):
"""Check TETRA results are concordant with JSpecies."""
# Perform TETRA analysis
zscores = dict()
for filename in paths_concordance_fna:
zscores[filename.stem] = tetra.calculate_tetra_zscore(filename)
results = tetra.calculate_correlations(zscores).values
# Compare JSpecies output
tgt_mat = parse_jspecies(path_concordance_jspecies)["Tetra"].values
assert results - tgt_mat == pytest.approx(0, abs=tolerance_tetra)
def test_tetra_concordance(self):
"""TETRA results concordant with JSpecies."""
# Perform TETRA analysis
zscores = dict()
for filename in self.infiles:
org = os.path.splitext(os.path.split(filename)[-1])[0]
zscores[org] = tetra.calculate_tetra_zscore(filename)
results = tetra.calculate_correlations(zscores)
results.to_csv(os.path.join(self.outdir, "pyani_tetra.tab"), sep="\t")
# Compare JSpecies output
diffmat = results.values - self.target["Tetra"].values
tetra_diff = pd.DataFrame(diffmat, index=results.index, columns=results.columns)
tetra_diff.to_csv(os.path.join(self.outdir, "pyani_tetra_diff.tab"), sep="\t")
assert_less(tetra_diff.abs().values.max(), self.tolerance["TETRA"])
def test_tetra_concordance(self):
"""Check TETRA results are concordant with JSpecies."""
# Perform TETRA analysis
zscores = dict()
for filename in self.infiles:
zscores[filename.stem] = tetra.calculate_tetra_zscore(filename)
results = tetra.calculate_correlations(zscores)
results.to_csv(self.outdir / "pyani_tetra.tab", sep="\t")
# Compare JSpecies output
diffmat = results.values - self.target["Tetra"].values
tetra_diff = pd.DataFrame(diffmat,
index=results.index,
columns=results.columns)
tetra_diff.to_csv(self.outdir / "pyani_tetra_diff.tab", sep="\t")
self.assertLess(tetra_diff.abs().values.max(), self.tolerance["TETRA"])
def test_tetra_concordance():
"""Test concordance of TETRA method with JSpecies output."""
# Make/check output directory
mode = "TETRA"
outdirname = make_outdir(mode)
# Get dataframes of JSpecies output
tetra_jspecies = parse_table(JSPECIES_OUTFILE, 'Tetra')
# Identify our input files, and the total lengths of each organism seq
infiles = pyani_files.get_fasta_files(INDIRNAME)
org_lengths = pyani_files.get_sequence_lengths(infiles)
# Test TETRA concordance
tetra_zscores = {}
for filename in infiles:
org = os.path.splitext(os.path.split(filename)[-1])[0]
tetra_zscores[org] = tetra.calculate_tetra_zscore(filename)
tetra_correlations = tetra.calculate_correlations(tetra_zscores)
index, columns = tetra_correlations.index, tetra_correlations.columns
tetra_diff = pd.DataFrame(tetra_correlations.as_matrix() -\
tetra_jspecies.as_matrix(),
index=index, columns=columns)
# Write dataframes to file, for reference
tetra_correlations.to_csv(os.path.join(outdirname,
'tetra_correlations.tab'),
sep='\t')
tetra_jspecies.to_csv(os.path.join(outdirname,
'tetra_jspecies.tab'),
sep='\t')
tetra_diff.to_csv(os.path.join(outdirname,
'tetra_diff.tab'),
sep='\t')
print "TETRA concordance test output placed in %s" % outdirname
print tetra_correlations, tetra_jspecies, tetra_diff
# We'd like the absolute difference reported to be < TETRA_THRESHOLD
max_diff = tetra_diff.abs().values.max()
print "Maximum difference for TETRA: %e" % max_diff
assert_less(max_diff, TETRA_THRESHOLD)
def test_tetra_concordance():
"""Test concordance of TETRA method with JSpecies output."""
# Make/check output directory
mode = "TETRA"
outdirname = delete_and_remake_outdir(mode)
# Get dataframes of JSpecies output
tetra_jspecies = parse_table(JSPECIES_OUTFILE, 'Tetra')
# Identify our input files, and the total lengths of each organism seq
infiles = pyani_files.get_fasta_files(INDIRNAME)
org_lengths = pyani_files.get_sequence_lengths(infiles)
# Test TETRA concordance
tetra_zscores = {}
for filename in infiles:
org = os.path.splitext(os.path.split(filename)[-1])[0]
tetra_zscores[org] = tetra.calculate_tetra_zscore(filename)
tetra_correlations = tetra.calculate_correlations(tetra_zscores)
index, columns = tetra_correlations.index, tetra_correlations.columns
tetra_diff = pd.DataFrame(tetra_correlations.as_matrix() -\
tetra_jspecies.as_matrix(),
index=index, columns=columns)
# Write dataframes to file, for reference
tetra_correlations.to_csv(os.path.join(outdirname,
'tetra_correlations.tab'),
sep='\t')
tetra_jspecies.to_csv(os.path.join(outdirname, 'tetra_jspecies.tab'),
sep='\t')
tetra_diff.to_csv(os.path.join(outdirname, 'tetra_diff.tab'), sep='\t')
print("TETRA concordance test output placed in %s" % outdirname)
print("TETRA correlations:\n", tetra_correlations)
print("TETRA JSpecies:\n", tetra_jspecies)
print("TETRA diff:\n", tetra_diff)
# We'd like the absolute difference reported to be < TETRA_THRESHOLD
max_diff = tetra_diff.abs().values.max()
print("Maximum difference for TETRA: %e" % max_diff)
assert_less(max_diff, TETRA_THRESHOLD)
def test_zscore(dir_seq, dir_targets):
"""Test that TETRA Z-score calculated correctly."""
tetra_z = calculate_tetra_zscore(dir_seq / "NC_002696.fna")
with (dir_targets / "tetra" / "zscore.json").open("r") as ifh:
target = json.load(ifh)
assert ordered(tetra_z) == ordered(target)
def test_zscore(self):
"""Test that TETRA Z-score calculated correctly."""
tetra_z = tetra.calculate_tetra_zscore(self.infile)
with (self.tgtdir / "zscore.json").open("r") as ifh:
target = json.load(ifh)
self.assertEqual(ordered(tetra_z), ordered(target))
def test_zscore(self):
"""TETRA Z-score calculated correctly."""
tetra_z = tetra.calculate_tetra_zscore(self.infile)
with open(os.path.join(self.tgtdir, 'zscore.json'), 'r') as ifh:
target = json.load(ifh)
assert_equal(ordered(tetra_z), ordered(target))