def rank_median_rd(self, phylum_rel_dists, taxa_for_dist_inference):
"""Calculate median relative divergence for each rank.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
"""
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
median_for_rank = {}
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
v = [
np_median(dists)
for taxon, dists in medians_for_taxa[rank].items()
if taxon in taxa_for_dist_inference
]
if v:
median_for_rank[rank] = np_median(v)
return median_for_rank
def compute(self):
"""Detect RFI
"""
median_size = (self.median_size_time, self.median_size_freq)
data = self.data - sp_dip.median_filter(self.data, size=median_size)
# data1 = np.abs(np.sum(data,0))
# data1 = np.abs(np.median(data,0))
data1 = (np_median(data, 0))
# th = np.percentile(data1, th_prctile)
thl = []
for ii in xrange(data1.shape[0] - 9):
thl.append(prctile(data1[ii:ii + 10], p=90))
# thl.append(max(data1[ii:ii+10]))
th = self.th_k * np_median(thl)
for ii in xrange(data1.shape[0]):
if data1[ii] > th:
z, p_value = sp_normaltest(data[:, ii])
if p_value < self.p_th:
if self.is_out_selected('Not_normal'):
self.flag_results['Not_normal'].flag_data[:, ii] = 1
else:
if self.is_out_selected('Normal'):
self.flag_results['Normal'].flag_data[:, ii] = 1
return self.flag_results
def makeBinDist(self, transformedCP, averageCoverages, kmerNormPC1, kmerPCs, contigGCs, contigLengths):
"""Determine the distribution of the points in this bin
The distribution is largely normal, except at the boundaries.
"""
#print "MBD", self.id, self.binSize
self.binSize = self.rowIndices.shape[0]
if(0 == np.size(self.rowIndices)):
return
# get the centroids
(self.covMedians, self.covStdevs) = self.getCentroidStats(transformedCP)
(self.lengthMean, self.lengthStd) = self.getCentroidStats(contigLengths)
self.kValMeanNormPC1 = np_median(kmerPCs[self.rowIndices])
self.kValStdevNormPC1 = np_std(kmerPCs[self.rowIndices])
self.kMedian = np_median(kmerPCs[self.rowIndices], axis=0)
self.kStdevs = np_std(kmerPCs[self.rowIndices], axis=0)
cvals = self.getAverageCoverageDist(averageCoverages)
self.cValMedian = np_around(np_median(cvals), decimals=3)
self.cValStdev = np_around(np_std(cvals), decimals=3)
self.gcMedian = np_median(contigGCs[self.rowIndices])
self.gcStdev = np_std(contigGCs[self.rowIndices])
# work out the total size
self.totalBP = sum([contigLengths[i] for i in self.rowIndices])
# set the acceptance ranges
self.makeLimits()
def makeBinDist(self, transformedCP, averageCoverages, kmerNormPC1,
kmerPCs, contigGCs, contigLengths):
"""Determine the distribution of the points in this bin
The distribution is largely normal, except at the boundaries.
"""
#print("MBD", self.id, self.binSize)
self.binSize = self.rowIndices.shape[0]
if (0 == np.size(self.rowIndices)):
return
# get the centroids
(self.covMedians,
self.covStdevs) = self.getCentroidStats(transformedCP)
(self.lengthMean,
self.lengthStd) = self.getCentroidStats(contigLengths)
self.kValMeanNormPC1 = np_median(kmerPCs[self.rowIndices])
self.kValStdevNormPC1 = np_std(kmerPCs[self.rowIndices])
self.kMedian = np_median(kmerPCs[self.rowIndices], axis=0)
self.kStdevs = np_std(kmerPCs[self.rowIndices], axis=0)
cvals = self.getAverageCoverageDist(averageCoverages)
self.cValMedian = np_around(np_median(cvals), decimals=3)
self.cValStdev = np_around(np_std(cvals), decimals=3)
self.gcMedian = np_median(contigGCs[self.rowIndices])
self.gcStdev = np_std(contigGCs[self.rowIndices])
# work out the total size
self.totalBP = sum([contigLengths[i] for i in self.rowIndices])
# set the acceptance ranges
self.makeLimits()
def mad(arr):
""" Median Absolute Deviation: a "Robust" version of standard deviation.
Indices variabililty of the sample.
https://en.wikipedia.org/wiki/Median_absolute_deviation
"""
arr = np.ma.array(
arr).compressed() # should be faster to not use masked arrays.
med = np_median(arr)
return np_median(np_abs(arr - med))
def create_feat_mat_1(graph):
CCs = list(nx_clustering(graph).values())
DCs = list(nx_average_neighbor_degree(graph).values())
degrees = [tup[1] for tup in graph.degree()]
edge_wts = [tup[2] for tup in graph.edges.data('weight')]
A_mat = nx_to_numpy_matrix(graph)
svs = np_linalg_svd(A_mat, full_matrices=False, compute_uv=False)
if len(svs) >= 3:
sv1 = svs[0]
sv2 = svs[1]
sv3 = svs[2]
elif len(svs) >= 2:
sv1 = svs[0]
sv2 = svs[1]
sv3 = 0
else:
sv1 = svs[0]
sv2 = sv3 = 0
feat_mat = np_vstack(
(nx_density(graph), nx_number_of_nodes(graph), max(degrees),
np_mean(degrees), np_median(degrees), np_var(degrees), max(CCs),
np_mean(CCs), np_var(CCs), np_mean(edge_wts), max(edge_wts),
np_var(edge_wts), np_mean(DCs), np_var(DCs), max(DCs), sv1, sv2,
sv3)).T
return feat_mat
def _write_rd_tree(self, tree, rel_node_dists, output_tree):
"""Write out tree with RED specified at each internal node."""
# copy tree so node labels aren't changed in original tree
red_tree = copy.deepcopy(tree)
for node_id, n in enumerate(red_tree.preorder_node_iter()):
if n == red_tree.seed_node:
red = 0
else:
red = np_median(rel_node_dists[node_id])
red_str = "|RED={:.3f}".format(red)
if n.is_leaf():
n.taxon.label += red_str
else:
if n.label:
n.label += red_str
else:
n.label = red_str
red_tree.write_to_path(output_tree,
schema='newick',
suppress_rooting=True,
unquoted_underscores=True)
def diff_on_off(on_off, i_start=0, i_stop=-1):
if i_start < 0:
i_start = len(on_off) + i_start
if i_stop < 0:
i_stop = len(on_off) + i_stop
n_samp = []
for ii in xrange(i_start, i_stop):
n_samp.append(on_off[on_off.keys()[ii]].data[DATA_KEYS[0]].shape[0])
n_samp = min(n_samp)
print n_samp
data_diff = {}
for dkey in DATA_KEYS:
data_diff[dkey] = []
for ii in xrange(i_start, i_stop, 2):
for dkey in DATA_KEYS:
print(
str(ii) + ": " + on_off[on_off.keys()[ii]].state + " " +
on_off[on_off.keys()[ii + 1]].state)
data_diff[dkey].append(
on_off[on_off.keys()[ii]].data[dkey][:n_samp, :] -
on_off[on_off.keys()[ii + 1]].data[dkey][:n_samp, :])
for dkey in DATA_KEYS:
data_diff[dkey] = np_median(np_array(data_diff[dkey]), 0)
return data_diff
def aggregateResources(self, nbins=20):
""" returns a json object which contains max, min, mean, median,
and the histogram itself for all memories/cpu
WARNING: this method is not particularly efficient
and shouldn't be used lightly!
"""
allData = {"memory": {"data": []}, "cpu": {"data": []}}
query = JobInstance.objects.filter(job=self).only("cpu").only("memory")
if query.count():
for inst in query:
agg = inst.aggregateResources()
for key in ['cpu', 'memory']:
if len(agg[key]):
allData[key]['data'].append(max(agg[key]))
del query
# finished aggregation, now we can do calculations
for key in allData:
d = allData[key]["data"]
allData[key]["max"] = max(d)
allData[key]["min"] = min(d)
arr = np_array(d, dtype=float)
allData[key]["mean"] = float(np_mean(arr, axis=0))
allData[key]["median"] = float(np_median(arr, axis=0))
hist, bins = np_hist(arr, nbins)
center = (bins[:-1] + bins[1:]) / 2
w = (bins[1] - bins[0])
histo = np_array([center, hist])
allData[key]['histogram'] = {
"histo": histo.tolist(),
"histoT": histo.T.tolist(),
"binWidth": float(w)
}
del allData[key]['data']
return dumps(allData)
def noise_dwt(cls, coeff, w):
"""Return the estimation of the DWT components noise level
coeff: DWT coefficients
w: pywt wavelet object
"""
n_boot = 1000
k_th = 10
k_std = 1. / np_sqrt(2)
std_l = []
std_a = np_zeros(n_boot)
wcomp = cls.wavecomp(coeff, w, len(coeff) - 1)
for ii in xrange(n_boot):
std_a[ii] = np_std(bootstrap_resample(wcomp, 10))
stdv = np_median(std_a)
std_l.append(stdv)
for ll in xrange(len(coeff) - 2, 0, -1):
stdv = stdv * k_std
std_l.append(stdv)
std_l.append(0)
std_l.reverse()
return np_array(std_l) * k_th
def test_median():
for dtype in NUMERIC_TYPES:
for shape in ((10,), (10, 11), (10, 11, 12)):
X = (100 * (np.random.random(shape) - .5)).astype(dtype)
for a in range(X.ndim):
assert_array_equal(_median(X, axis=a).squeeze(),
np_median(X.astype(np.float64), axis=a))
def test_median():
for dtype in NUMERIC_TYPES:
for shape in ((10, ), (10, 11), (10, 11, 12)):
X = (100 * (np.random.random(shape) - .5)).astype(dtype)
for a in range(X.ndim):
assert_array_equal(
_median(X, axis=a).squeeze(),
np_median(X.astype(np.float64), axis=a))
def _median_rank_rd(self,
tree,
placed_taxon,
taxonomy,
trusted_taxa_file,
min_children,
min_support):
"""Calculate median relative divergence to each node and thresholds for each taxonomic rank.
Parameters
----------
tree : Tree
Dendropy Tree.
placed_taxon : set
Taxon currently placed in tree which can be used for relative divergence inference.
taxonomy: d[taxon_id] -> taxonomy info
Taxonomic information for extant taxa.
trusted_taxa_file : str
File specifying trusted taxa to consider when inferring distribution. Set to None to consider all taxa.
min_children : int
Only consider taxa with at least the specified number of children taxa when inferring distribution.
min_support : float
Only consider taxa with at least this level of support when inferring distribution.
Returns
-------
d[rank_index] -> float
Median relative divergence for each taxonomic rank.
"""
# read trusted taxa
trusted_taxa = None
if trusted_taxa_file:
trusted_taxa = read_taxa_file(trusted_taxa_file)
# determine taxa to be used for inferring distribution
taxa_for_dist_inference = filter_taxa_for_dist_inference(tree,
taxonomy,
trusted_taxa,
min_children,
min_support)
taxa_for_dist_inference.intersection_update(placed_taxon)
# infer distribution
outliers = Outliers()
phylum_rel_dists, rel_node_dists = outliers.median_rd_over_phyla(tree,
taxa_for_dist_inference,
taxonomy)
median_for_rank = outliers.rank_median_rd(phylum_rel_dists,
taxa_for_dist_inference)
# set edge lengths to median value over all rootings
tree.seed_node.rel_dist = 0.0
for n in tree.preorder_node_iter(lambda n: n != tree.seed_node):
n.rel_dist = np_median(rel_node_dists[n.id])
return median_for_rank
def _median_rank_rd(self,
tree,
placed_taxon,
taxonomy,
trusted_taxa_file,
min_children,
min_support):
"""Calculate median relative divergence to each node and thresholds for each taxonomic rank.
Parameters
----------
tree : Tree
Dendropy Tree.
placed_taxon : set
Taxon currently placed in tree which can be used for relative divergence inference.
taxonomy: d[taxon_id] -> taxonomy info
Taxonomic information for extant taxa.
trusted_taxa_file : str
File specifying trusted taxa to consider when inferring distribution. Set to None to consider all taxa.
min_children : int
Only consider taxa with at least the specified number of children taxa when inferring distribution.
min_support : float
Only consider taxa with at least this level of support when inferring distribution.
Returns
-------
d[rank_index] -> float
Median relative divergence for each taxonomic rank.
"""
# read trusted taxa
trusted_taxa = None
if trusted_taxa_file:
trusted_taxa = read_taxa_file(trusted_taxa_file)
# determine taxa to be used for inferring distribution
taxa_for_dist_inference = filter_taxa_for_dist_inference(tree,
taxonomy,
trusted_taxa,
min_children,
min_support)
taxa_for_dist_inference.intersection_update(placed_taxon)
# infer distribution
outliers = Outliers()
phylum_rel_dists, rel_node_dists = outliers.median_rd_over_phyla(tree,
taxa_for_dist_inference,
taxonomy)
median_for_rank = outliers.rank_median_rd(phylum_rel_dists,
taxa_for_dist_inference)
# set edge lengths to median value over all rootings
tree.seed_node.rel_dist = 0.0
for n in tree.preorder_node_iter(lambda n: n != tree.seed_node):
n.rel_dist = np_median(rel_node_dists[n.id])
return median_for_rank
def rank_median_rd(self, phylum_rel_dists, taxa_for_dist_inference):
"""Calculate median relative divergence for each rank.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
"""
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
median_for_rank = {}
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
v = [np_median(dists) for taxon, dists in medians_for_taxa[rank].iteritems() if taxon in taxa_for_dist_inference]
median_for_rank[rank] = np_median(v)
return median_for_rank
def getCentroidStats(self, profile):
"""Calculate the centroids of the profile"""
working_list = profile[self.rowIndices]
# return the mean and stdev
# we divide by std so we need to make sure it's never 0
tmp_stds = np_std(working_list, axis=0)
mean_std = np_mean(tmp_stds)
try:
std = np_array([x if x != 0 else mean_std for x in tmp_stds])
except:
std = mean_std
return (np_median(working_list,axis=0), std)
def getCentroidStats(self, profile):
"""Calculate the centroids of the profile"""
working_list = profile[self.rowIndices]
# return the mean and stdev
# we divide by std so we need to make sure it's never 0
tmp_stds = np_std(working_list, axis=0)
mean_std = np_mean(tmp_stds)
try:
std = np_array([x if x != 0 else mean_std for x in tmp_stds])
except:
std = mean_std
return (np_median(working_list, axis=0), std)
def rep_genome_stats(self, clusters, genome_files):
"""Calculate statistics relative to representative genome."""
self.logger.info('Calculating statistics to cluster representatives:')
stats = {}
for idx, (rid, cids) in enumerate(clusters.items()):
if len(cids) == 0:
stats[rid] = self.RepStats(min_ani=-1,
mean_ani=-1,
std_ani=-1,
median_ani=-1)
else:
# calculate ANI to representative genome
gid_pairs = []
for cid in cids:
gid_pairs.append((cid, rid))
gid_pairs.append((rid, cid))
if True: # *** DEBUGGING
ani_af = self.fastani.pairs(gid_pairs,
genome_files,
report_progress=False)
else:
ani_af = self.fastani.ani_cache
# calculate statistics
anis = [FastANI.symmetric_ani(ani_af, cid, rid)[
0] for cid in cids]
stats[rid] = self.RepStats(min_ani=min(anis),
mean_ani=np_mean(anis),
std_ani=np_std(anis),
median_ani=np_median(anis))
statusStr = '-> Processing %d of %d (%.2f%%) clusters.'.ljust(86) % (
idx+1,
len(clusters),
float((idx+1)*100)/len(clusters))
sys.stdout.write('%s\r' % statusStr)
sys.stdout.flush()
sys.stdout.write('\n')
return stats
def compute(self):
"""Detect RFI
"""
m_ind = {'L': 0, 'R': 1, 'Q': 2, 'U': 3}
if self.num_of_rms_above_median[0] <= self.num_of_rms_above_median[
1] or self.num_of_rms_above_median[
0] >= self.num_of_rms_above_median[2]:
raise ValueError
return 0
for lab in self.flag_results.keys():
med = np_median(self.data[m_ind[lab]][self.data[m_ind[lab]] > 10])
rms = np_sqrt(((self.data[m_ind[lab]][self.data[m_ind[lab]] > 10] -
med)**2).mean())
res = sp_threshold(self.data[m_ind[lab]] - med,
threshmin=self.num_of_rms_above_median[0] * rms,
newval=0)
res[res > 0] = 1
self.flag_results[lab].pola = lab
self.flag_results[lab].flag_data = res
return self.flag_results
def _rep_genome_stats(self, clusters, genome_files):
"""Calculate statistics relative to representative genome."""
self.logger.info('Calculating statistics to cluster representatives:')
stats = {}
for idx, (rid, cids) in enumerate(clusters.items()):
if len(cids) == 0:
stats[rid] = self.RepStats(min_ani = -1,
mean_ani = -1,
std_ani = -1,
median_ani = -1)
else:
# calculate ANI to representative genome
gid_pairs = []
for cid in cids:
gid_pairs.append((cid, rid))
ani_af = self.ani_cache.fastani_pairs(gid_pairs,
genome_files,
report_progress=False)
# calculate statistics
anis = [ani_af[cid][rid][0] for cid in cids]
stats[rid] = self.RepStats(min_ani = min(anis),
mean_ani = np_mean(anis),
std_ani = np_std(anis),
median_ani = np_median(anis))
statusStr = '-> Processing %d of %d (%.2f%%) clusters.'.ljust(86) % (
idx+1,
len(clusters),
float((idx+1)*100)/len(clusters))
sys.stdout.write('%s\r' % statusStr)
sys.stdout.flush()
sys.stdout.write('\n')
return stats
def _median_summary_outlier_file(self, phylum_rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks, outlier_table,
rank_file, verbose_table):
"""Identify outliers relative to the median of rank distributions.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
gtdb_parent_ranks: d[taxon] -> string indicating parent taxa
Parent taxa for each taxon.
outlier_table : str
Desired name of output table.
rank_file : str
Desired name of file indicating median relative distance of each rank.
verbose_table : boolean
Print additional columns in output table.
"""
# determine median relative distance for each taxa
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
# determine median relative distance for each rank
median_for_rank = self.rank_median_rd(phylum_rel_dists,
taxa_for_dist_inference)
with open(rank_file, 'w') as fout_rank:
median_str = []
for rank in sorted(median_for_rank.keys()):
median_str.append('"' + Taxonomy.rank_labels[rank] + '":' +
str(median_for_rank[rank]))
fout_rank.write('{' + ','.join(median_str) + '}\n')
fout = open(outlier_table, 'w')
if verbose_table:
fout.write('Taxa\tGTDB taxonomy\tMedian distance')
fout.write('\tMedian of rank\tMedian difference')
fout.write('\tClosest rank\tClassifciation\n')
else:
fout.write(
'Taxa\tGTDB taxonomy\tMedian distance\tMedian difference\tClosest rank\tClassification\n'
)
for rank in sorted(median_for_rank.keys()):
for clade_label, dists in medians_for_taxa[rank].items():
dists = np_array(dists)
taxon_median = np_median(dists)
delta = taxon_median - median_for_rank[rank]
closest_rank_dist = 1e10
for test_rank, test_median in median_for_rank.items():
abs_dist = abs(taxon_median - test_median)
if abs_dist < closest_rank_dist:
closest_rank_dist = abs_dist
closest_rank = Taxonomy.rank_labels[test_rank]
classification = "OK"
if delta < -0.2:
classification = "very overclassified"
elif delta < -0.1:
classification = "overclassified"
elif delta > 0.2:
classification = "very underclassified"
elif delta > 0.1:
classification = "underclassified"
if verbose_table:
fout.write(
'%s\t%s\t%.2f\t%.3f\t%.3f\t%s\t%s\n' %
(clade_label, ';'.join(gtdb_parent_ranks[clade_label]),
taxon_median, median_for_rank[rank], delta,
closest_rank, classification))
else:
fout.write(
'%s\t%s\t%.3f\t%.3f\t%s\t%s\n' %
(clade_label, ';'.join(gtdb_parent_ranks[clade_label]),
taxon_median, delta, closest_rank, classification))
fout.close()
def _distribution_summary_plot(self, phylum_rel_dists,
taxa_for_dist_inference, plot_file):
"""Summary plot showing the distribution of taxa at each taxonomic rank under different rootings.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
plot_file : str
Desired name of output plot.
"""
self.fig.clear()
self.fig.set_size_inches(12, 6)
ax = self.fig.add_subplot(111)
# determine median relative distance for each taxa
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
# create percentile and classification boundary lines
percentiles = {}
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
v = [
np_median(dists)
for taxon, dists in medians_for_taxa[rank].items()
if taxon in taxa_for_dist_inference
]
if not v:
# not taxa at rank suitable for creating classification
# boundaries
continue
p10, p50, p90 = np_percentile(v, [10, 50, 90])
ax.plot((p10, p10), (i, i + 0.25),
c=(0.3, 0.3, 0.3),
lw=2,
zorder=2)
ax.plot((p50, p50), (i, i + 0.5),
c=(0.3, 0.3, 0.3),
lw=2,
zorder=2)
ax.plot((p90, p90), (i, i + 0.25),
c=(0.3, 0.3, 0.3),
lw=2,
zorder=2)
for b in [-0.2, -0.1, 0.1, 0.2]:
boundary = p50 + b
if 1.0 > boundary > 0.0:
if abs(b) == 0.1:
c = (1.0, 0.65, 0.0) # orange
else:
c = (1.0, 0.0, 0.0)
ax.plot((boundary, boundary), (i, i + 0.5),
c=c,
lw=2,
zorder=2)
percentiles[i] = [p10, p50, p90]
# create scatter plot and results table
x = []
y = []
c = []
labels = []
rank_labels = []
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
rank_label = Taxonomy.rank_labels[rank]
rank_labels.append(rank_label +
' (%d)' % len(medians_for_taxa[rank]))
mono = []
poly = []
no_inference = []
for clade_label, dists in medians_for_taxa[rank].items():
md = np_median(dists)
x.append(md)
y.append(i)
labels.append(clade_label)
if self._is_integer(clade_label.split('^')[-1]):
# taxa with a numerical suffix after a caret indicate
# polyphyletic groups when decorated with tax2tree
c.append((1.0, 0.0, 0.0))
poly.append(md)
elif clade_label not in taxa_for_dist_inference:
c.append((0.3, 0.3, 0.3))
no_inference.append(md)
else:
c.append((0.0, 0.0, 1.0))
mono.append(md)
# histogram for each rank
n = 0
if len(mono) > 0:
mono = np_array(mono)
no_inference = np_array(no_inference)
poly = np_array(poly)
binwidth = 0.025
bins = np_arange(0, 1.0 + binwidth, binwidth)
mono_max_count = max(np_histogram(mono, bins=bins)[0])
mono_weights = np_ones_like(mono) * (1.0 / mono_max_count)
w = float(
len(mono)) / (len(mono) + len(poly) + len(no_inference))
n, b, p = ax.hist(mono,
bins=bins,
color=(0.0, 0.0, 1.0),
alpha=0.25,
weights=0.9 * w * mono_weights,
bottom=i,
lw=0,
zorder=0)
if len(no_inference) > 0:
no_inference_max_count = max(
np_histogram(no_inference, bins=bins)[0])
no_inference_weights = np_ones_like(no_inference) * (
1.0 / no_inference_max_count)
ax.hist(no_inference,
bins=bins,
color=(0.3, 0.3, 0.3),
alpha=0.25,
weights=0.9 * (1.0 - w) * no_inference_weights,
bottom=i + n,
lw=0,
zorder=0)
if len(poly) > 0:
poly_max_count = max(np_histogram(poly, bins=bins)[0])
poly_weights = np_ones_like(poly) * (1.0 / poly_max_count)
ax.hist(poly,
bins=bins,
color=(1.0, 0.0, 0.0),
alpha=0.25,
weights=0.9 * (1.0 - w) * poly_weights,
bottom=i + n,
lw=0,
zorder=0)
scatter = ax.scatter(x, y, alpha=0.5, s=48, c=c, zorder=1)
# set plot elements
ax.grid(color=(0.8, 0.8, 0.8), linestyle='dashed')
ax.set_xlabel('relative distance')
ax.set_xticks(np_arange(0, 1.05, 0.1))
ax.set_xlim([-0.01, 1.01])
ax.set_ylabel('rank (no. taxa)')
ax.set_yticks(list(range(0, len(medians_for_taxa))))
ax.set_ylim([-0.2, len(medians_for_taxa) - 0.01])
ax.set_yticklabels(rank_labels)
self.prettify(ax)
# make plot interactive
mpld3.plugins.clear(self.fig)
mpld3.plugins.connect(
self.fig, mpld3.plugins.PointLabelTooltip(scatter, labels=labels))
mpld3.plugins.connect(self.fig,
mpld3.plugins.MousePosition(fontsize=10))
mpld3.save_html(self.fig, plot_file[0:plot_file.rfind('.')] + '.html')
self.fig.tight_layout(pad=1)
self.fig.savefig(plot_file, dpi=self.dpi)
def pairwise_stats(self, clusters, genome_files):
"""Calculate statistics for all pairwise comparisons in a species cluster."""
self.logger.info(
f'Restricting pairwise comparisons to {self.max_genomes_for_stats:,} randomly selected genomes.')
self.logger.info(
'Calculating statistics for all pairwise comparisons in a species cluster:')
stats = {}
for idx, (rid, cids) in enumerate(clusters.items()):
statusStr = '-> Processing {:,} of {:,} ({:2f}%) clusters (size = {:,}).'.ljust(86).format(
idx+1,
len(clusters),
float((idx+1)*100)/len(clusters),
len(cids))
sys.stdout.write('{}\r'.format(statusStr))
sys.stdout.flush()
if len(cids) == 0:
stats[rid] = self.PairwiseStats(min_ani=-1,
mean_ani=-1,
std_ani=-1,
median_ani=-1,
ani_to_medoid=-1,
mean_ani_to_medoid=-1,
mean_ani_to_rep=-1,
ani_below_95=-1)
else:
if len(cids) > self.max_genomes_for_stats:
cids = set(random.sample(cids, self.max_genomes_for_stats))
# calculate ANI to representative genome
gid_pairs = []
gids = list(cids.union([rid]))
for gid1, gid2 in combinations(gids, 2):
gid_pairs.append((gid1, gid2))
gid_pairs.append((gid2, gid1))
if True: # ***DEBUGGING
ani_af = self.fastani.pairs(gid_pairs,
genome_files,
report_progress=False)
else:
ani_af = self.fastani.ani_cache
# calculate medoid point
if len(gids) > 2:
dist_mat = np_zeros((len(gids), len(gids)))
for i, gid1 in enumerate(gids):
for j, gid2 in enumerate(gids):
if i < j:
ani, _af = FastANI.symmetric_ani(
ani_af, gid1, gid2)
dist_mat[i, j] = 100 - ani
dist_mat[j, i] = 100 - ani
medoid_idx = np_argmin(dist_mat.sum(axis=0))
medoid_gid = gids[medoid_idx]
else:
# with only 2 genomes in a cluster, the representative is the
# natural medoid at least for reporting statistics for the
# individual species cluster
medoid_gid = rid
mean_ani_to_medoid = np_mean([FastANI.symmetric_ani(ani_af, gid, medoid_gid)[0]
for gid in gids if gid != medoid_gid])
mean_ani_to_rep = np_mean([FastANI.symmetric_ani(ani_af, gid, rid)[0]
for gid in gids if gid != rid])
if mean_ani_to_medoid < mean_ani_to_rep:
self.logger.error('mean_ani_to_medoid < mean_ani_to_rep')
sys.exit(-1)
# calculate statistics
anis = []
for gid1, gid2 in combinations(gids, 2):
ani, _af = FastANI.symmetric_ani(ani_af, gid1, gid2)
anis.append(ani)
stats[rid] = self.PairwiseStats(
min_ani=min(anis),
mean_ani=np_mean(anis),
std_ani=np_std(anis),
median_ani=np_median(anis),
ani_to_medoid=FastANI.symmetric_ani(
ani_af, rid, medoid_gid)[0],
mean_ani_to_medoid=mean_ani_to_medoid,
mean_ani_to_rep=mean_ani_to_rep,
ani_below_95=sum([1 for ani in anis if ani < 95]))
sys.stdout.write('\n')
return stats
def run(self, scaffold_stats):
"""Calculate statistics for genomes.
Parameters
----------
scaffold_stats : ScaffoldStats
Statistics for individual scaffolds.
"""
self.logger.info(
"Calculating statistics for {:,} genomes over {:,} scaffolds.".
format(scaffold_stats.num_genomes(),
scaffold_stats.num_scaffolds()))
self.coverage_headers = scaffold_stats.coverage_headers
self.signature_headers = scaffold_stats.signature_headers
genome_size = defaultdict(int)
scaffold_length = defaultdict(list)
gc = defaultdict(list)
coverage = defaultdict(list)
signature = defaultdict(list)
for _scaffold_id, stats in scaffold_stats.stats.items():
if stats.genome_id == scaffold_stats.unbinned:
continue
genome_size[stats.genome_id] += stats.length
scaffold_length[stats.genome_id].append(stats.length)
gc[stats.genome_id].append(stats.gc)
coverage[stats.genome_id].append(stats.coverage)
signature[stats.genome_id].append(stats.signature)
# record statistics for each genome
genomic_signature = GenomicSignature(0)
self.genome_stats = {}
for genome_id in genome_size:
# calculate weighted mean and median statistics
weights = np_array(scaffold_length[genome_id])
len_array = np_array(scaffold_length[genome_id])
mean_len = ws.numpy_weighted_mean(len_array, weights)
median_len = ws.numpy_weighted_median(len_array, weights)
gc_array = np_array(gc[genome_id])
mean_gc = ws.numpy_weighted_mean(gc_array, weights)
median_gc = ws.numpy_weighted_median(gc_array, weights)
cov_array = np_array(coverage[genome_id]).T
mean_cov = ws.numpy_weighted_mean(cov_array, weights)
median_cov = []
for i in range(cov_array.shape[0]):
median_cov.append(
ws.numpy_weighted_median(cov_array[i, :], weights))
signature_array = np_array(signature[genome_id]).T
mean_signature = ws.numpy_weighted_mean(signature_array, weights)
# calculate mean and median tetranucleotide distance
td = []
for scaffold_id in scaffold_stats.scaffolds_in_genome[genome_id]:
stats = scaffold_stats.stats[scaffold_id]
td.append(
genomic_signature.manhattan(stats.signature,
mean_signature))
self.genome_stats[genome_id] = self.GenomeStats(
genome_size[genome_id], mean_len, median_len, mean_gc,
median_gc, mean_cov, median_cov, mean_signature, np_mean(td),
np_median(td))
return self.genome_stats
def run(self, input_tree,
taxonomy_file,
output_dir,
plot_taxa_file,
plot_dist_taxa_only,
plot_domain,
highlight_polyphyly,
highlight_taxa_file,
trusted_taxa_file,
fixed_root,
min_children,
min_support,
mblet,
fmeasure_table,
min_fmeasure,
fmeasure_mono,
verbose_table):
"""Determine distribution of taxa at each taxonomic rank.
Parameters
----------
input_tree : str
Name of input tree.
taxonomy_file : str
File with taxonomy strings for each taxa.
output_dir : str
Desired output directory.
plot_taxa_file : str
File specifying taxa to plot. Set to None to consider all taxa.
plot_dist_taxa_only : boolean
Only plot the taxa used to infer distribution.
plot_domain : boolean
Plot domain rank.
trusted_taxa_file : str
File specifying trusted taxa to consider when inferring distribution. Set to None to consider all taxa.
fixed_root : boolean
Usa a single fixed root to infer outliers.
min_children : int
Only consider taxa with at least the specified number of children taxa when inferring distribution.
min_support : float
Only consider taxa with at least this level of support when inferring distribution.
verbose_table : boolean
Print additional columns in output table.
"""
# read tree
self.logger.info('Reading tree.')
tree = dendropy.Tree.get_from_path(input_tree,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
input_tree_name = os.path.splitext(os.path.basename(input_tree))[0]
# pull taxonomy from tree and file
self.logger.info('Reading taxonomy.')
taxonomy = Taxonomy().read(taxonomy_file)
tree_taxonomy = Taxonomy().read_from_tree(input_tree,
warnings=False)
gtdb_parent_ranks = Taxonomy().parents(tree_taxonomy)
# read trusted taxa
trusted_taxa = None
if trusted_taxa_file:
trusted_taxa = read_taxa_file(trusted_taxa_file)
# read F-measure for taxa
fmeasure = None
if fmeasure_table:
fmeasure = self.read_fmeasure(fmeasure_table)
# determine taxa to be used for inferring distribution
taxa_for_dist_inference = filter_taxa_for_dist_inference(tree,
taxonomy,
trusted_taxa,
min_children,
min_support,
fmeasure,
min_fmeasure)
# limit plotted taxa
taxa_to_plot = None
if plot_dist_taxa_only:
taxa_to_plot = taxa_for_dist_inference
elif plot_taxa_file:
taxa_to_plot = read_taxa_file(plot_taxa_file)
else:
# plot every taxon defined in tree
taxa_to_plot = set()
for node in tree.preorder_node_iter():
support, taxon, _auxiliary_info = parse_label(node.label)
if taxon:
taxon = taxon.split(';')[-1].strip() # get most specific taxon from compound names
# (e.g. p__Armatimonadetes; c__Chthonomonadetes)
taxa_to_plot.add(taxon)
if False:
# HACK FOR NCBI: only plot taxa with >= 2 taxa
taxa_to_plot = set()
for node in tree.preorder_node_iter():
if not node.label or node.is_leaf():
continue
support, taxon, _auxiliary_info = parse_label(node.label)
if not taxon:
continue
taxon = taxon.split(';')[-1].strip() # get most specific taxon from compound names
# (e.g. p__Armatimonadetes; c__Chthonomonadetes)
# count number of subordinate children
rank_prefix = taxon[0:3]
if min_children > 0 and rank_prefix != 's__':
child_rank_index = Taxonomy().rank_index[rank_prefix] + 1
child_rank_prefix = Taxonomy.rank_prefixes[child_rank_index]
subordinate_taxa = set()
for leaf in node.leaf_iter():
taxa = taxonomy.get(leaf.taxon.label, Taxonomy.rank_prefixes)
if len(taxa) > child_rank_index:
sub_taxon = taxa[child_rank_index]
if sub_taxon != Taxonomy.rank_prefixes[child_rank_index] and sub_taxon.startswith(child_rank_prefix):
subordinate_taxa.add(sub_taxon)
if len(subordinate_taxa) < min_children:
continue
taxa_to_plot.add(taxon)
# highlight taxa
highlight_taxa = set()
if highlight_taxa_file:
for line in open(highlight_taxa_file):
highlight_taxa.add(line.strip().split('\t')[0])
# check if a single fixed root should be used
if fixed_root or mblet:
self.logger.info('Using single fixed rooting for inferring distributions.')
if not mblet:
rel_dists = self.rd_fixed_root(tree, taxa_for_dist_inference)
else:
rel_dists = self.mblet(tree, taxa_for_dist_inference)
# create fixed rooting style tables and plots
distribution_table = os.path.join(output_dir, '%s.rank_distribution.tsv' % input_tree_name)
plot_file = os.path.join(output_dir, '%s.png' % input_tree_name)
self._distribution_plot(rel_dists,
taxa_for_dist_inference,
highlight_polyphyly,
highlight_taxa,
distribution_table,
fmeasure,
fmeasure_mono,
plot_file)
median_outlier_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
self._median_outlier_file(rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table)
else:
# calculate relative distance to taxa
rd = RelativeDistance()
rel_dists = rd.rel_dist_to_named_clades(tree)
# restrict to taxa of interest
if taxa_to_plot:
for r in rel_dists:
for k in set(rel_dists[r].keys()) - set(taxa_to_plot):
del rel_dists[r][k]
# report number of taxa at each rank
print ''
print 'Rank\tTaxa to Plot\tTaxa for Inference'
for rank, taxa in rel_dists.iteritems():
taxa_for_inference = [x for x in taxa if x in taxa_for_dist_inference]
print '%s\t%d\t%d' % (Taxonomy.rank_labels[rank], len(taxa), len(taxa_for_inference))
print ''
# *** determine phyla for inferring distribution
if True:
phylum_rel_dists, rel_node_dists = self.median_rd_over_phyla(tree,
taxa_for_dist_inference)
else:
phyla_for_inference = filter_taxa_for_dist_inference(tree,
taxonomy,
trusted_taxa,
2,
min_support,
fmeasure,
min_fmeasure)
phylum_rel_dists, rel_node_dists = self.median_rd_over_phyla(tree,
phyla_for_inference)
print ''
print 'Phyla for RED Inference:'
print ','.join(phylum_rel_dists)
phyla_file = os.path.join(output_dir, '%s.phyla.tsv' % input_tree_name)
fout = open(phyla_file, 'w')
for p in phylum_rel_dists:
fout.write(p + '\n')
fout.close()
# set edge lengths to median value over all rootings
tree.seed_node.rel_dist = 0.0
for n in tree.preorder_node_iter(lambda n: n != tree.seed_node):
n.rel_dist = np_median(rel_node_dists[n.id])
rd_to_parent = n.rel_dist - n.parent_node.rel_dist
if rd_to_parent < 0:
self.logger.warning('Not all branches are positive after scaling.')
n.edge_length = rd_to_parent
for phylum, rel_dists in phylum_rel_dists.iteritems():
phylum_dir = os.path.join(output_dir, phylum)
if not os.path.exists(phylum_dir):
os.makedirs(phylum_dir)
# restrict to taxa of interest
if taxa_to_plot:
for r in rel_dists:
for k in set(rel_dists[r].keys()) - set(taxa_to_plot):
del rel_dists[r][k]
# create distribution plot
distribution_table = os.path.join(phylum_dir, '%s.rank_distribution.tsv' % phylum)
plot_file = os.path.join(phylum_dir, '%s.rank_distribution.png' % phylum)
self._distribution_plot(rel_dists,
taxa_for_dist_inference,
highlight_polyphyly,
highlight_taxa,
distribution_table,
fmeasure,
fmeasure_mono,
plot_file)
median_outlier_table = os.path.join(phylum_dir, '%s.median_outlier.tsv' % phylum)
self._median_outlier_file(rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table)
plot_file = os.path.join(output_dir, '%s.png' % input_tree_name)
self._distribution_summary_plot(phylum_rel_dists,
taxa_for_dist_inference,
highlight_polyphyly,
highlight_taxa,
fmeasure,
fmeasure_mono,
plot_file)
median_outlier_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
median_rank_file = os.path.join(output_dir, '%s.dict' % input_tree_name)
self._median_summary_outlier_file(phylum_rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table,
median_rank_file,
verbose_table)
output_rd_file = os.path.join(output_dir, '%s.node_rd.tsv' % input_tree_name)
self._write_rd(tree, output_rd_file)
output_tree = os.path.join(output_dir, '%s.scaled.tree' % input_tree_name)
tree.write_to_path(output_tree,
schema='newick',
suppress_rooting=True,
unquoted_underscores=True)
def run(self, input_tree,
taxonomy_file,
output_dir,
plot_taxa_file,
plot_dist_taxa_only,
plot_domain,
trusted_taxa_file,
fixed_root,
min_children,
min_support,
verbose_table):
"""Determine distribution of taxa at each taxonomic rank.
Parameters
----------
input_tree : str
Name of input tree.
taxonomy_file : str
File with taxonomy strings for each taxa.
output_dir : str
Desired output directory.
plot_taxa_file : str
File specifying taxa to plot. Set to None to consider all taxa.
plot_dist_taxa_only : boolean
Only plot the taxa used to infer distribution.
plot_domain : boolean
Plot domain rank.
trusted_taxa_file : str
File specifying trusted taxa to consider when inferring distribution. Set to None to consider all taxa.
fixed_root : boolean
Usa a single fixed root to infer outliers.
min_children : int
Only consider taxa with at least the specified number of children taxa when inferring distribution.
min_support : float
Only consider taxa with at least this level of support when inferring distribution.
verbose_table : boolean
Print additional columns in output table.
"""
# read tree
self.logger.info('Reading tree.')
tree = dendropy.Tree.get_from_path(input_tree,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
input_tree_name = os.path.splitext(os.path.basename(input_tree))[0]
# pull taxonomy from tree
if not taxonomy_file:
self.logger.info('Reading taxonomy from tree.')
taxonomy_file = os.path.join(output_dir, '%s.taxonomy.tsv' % input_tree_name)
taxonomy = Taxonomy().read_from_tree(input_tree)
Taxonomy().write(taxonomy, taxonomy_file)
else:
self.logger.info('Reading taxonomy from file.')
taxonomy = Taxonomy().read(taxonomy_file)
gtdb_parent_ranks = Taxonomy().parents(taxonomy)
# read trusted taxa
trusted_taxa = None
if trusted_taxa_file:
trusted_taxa = read_taxa_file(trusted_taxa_file)
# determine taxa to be used for inferring distribution
taxa_for_dist_inference = filter_taxa_for_dist_inference(tree, taxonomy, trusted_taxa, min_children, min_support)
# limit plotted taxa
taxa_to_plot = None
if plot_dist_taxa_only:
taxa_to_plot = taxa_for_dist_inference
elif plot_taxa_file:
taxa_to_plot = read_taxa_file(plot_taxa_file)
# check if a single fixed root should be used
if fixed_root:
self.logger.info('Using single fixed rooting for inferring distributions.')
rel_dists = self.rd_fixed_root(tree, taxa_for_dist_inference)
# create fixed rooting style tables and plots
distribution_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
plot_file = os.path.join(output_dir, '%s.png' % input_tree_name)
self._distribution_plot(rel_dists, taxa_for_dist_inference, distribution_table, plot_file)
median_outlier_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
self._median_outlier_file(rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table)
else:
# calculate relative distance to taxa
rd = RelativeDistance()
rel_dists = rd.rel_dist_to_named_clades(tree)
# report number of taxa at each rank
print('')
print('Rank\tTaxa to Plot\tTaxa for Inference')
for rank, taxa in rel_dists.items():
taxa_for_inference = [x for x in taxa if x in taxa_for_dist_inference]
print('%s\t%d\t%d' % (Taxonomy.rank_labels[rank], len(taxa), len(taxa_for_inference)))
print('')
phylum_rel_dists, rel_node_dists = self.median_rd_over_phyla(tree,
taxa_for_dist_inference,
taxonomy)
# set edge lengths to median value over all rootings
tree.seed_node.rel_dist = 0.0
for n in tree.preorder_node_iter(lambda n: n != tree.seed_node):
n.rel_dist = np_median(rel_node_dists[n.id])
rd_to_parent = n.rel_dist - n.parent_node.rel_dist
if rd_to_parent < 0:
self.logger.warning('Not all branches are positive after scaling.')
n.edge_length = rd_to_parent
for phylum, rel_dists in phylum_rel_dists.items():
phylum_dir = os.path.join(output_dir, phylum)
if not os.path.exists(phylum_dir):
os.makedirs(phylum_dir)
# create distribution plot
distribution_table = os.path.join(phylum_dir, '%s.rank_distribution.tsv' % phylum)
plot_file = os.path.join(phylum_dir, '%s.rank_distribution.png' % phylum)
self._distribution_plot(rel_dists, taxa_for_dist_inference, distribution_table, plot_file)
median_outlier_table = os.path.join(phylum_dir, '%s.median_outlier.tsv' % phylum)
self._median_outlier_file(rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table)
plot_file = os.path.join(output_dir, '%s.png' % input_tree_name)
self._distribution_summary_plot(phylum_rel_dists, taxa_for_dist_inference, plot_file)
median_outlier_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
median_rank_file = os.path.join(output_dir, '%s.dict' % input_tree_name)
self._median_summary_outlier_file(phylum_rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table,
median_rank_file,
verbose_table)
output_rd_file = os.path.join(output_dir, '%s.node_rd.tsv' % input_tree_name)
self._write_rd(tree, output_rd_file)
output_tree = os.path.join(output_dir, '%s.scaled.tree' % input_tree_name)
tree.write_to_path(output_tree,
schema='newick',
suppress_rooting=True,
unquoted_underscores=True)
def _median_outlier_file(self,
rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
output_file):
"""Identify outliers relative to the median of rank distributions.
Parameters
----------
rel_dists: d[rank_index][taxon] -> relative divergence
Relative divergence of taxa at each rank.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
gtdb_parent_ranks: d[taxon] -> string indicating parent taxa
Parent taxa for each taxon.
output_file : str
Desired name of output table.
"""
# determine median relative distance for each rank
median_rel_dist = {}
for rank, d in rel_dists.items():
v = [dist for taxa, dist in d.items() if taxa in taxa_for_dist_inference]
if len(v) == 0:
continue
median_rel_dist[rank] = np_median(v)
fout = open(output_file, 'w')
fout.write('Taxa\tGTDB taxonomy\tMedian distance\tMean difference\tClosest rank\tClassification\n')
for i, rank in enumerate(sorted(rel_dists.keys())):
for clade_label, dist in rel_dists[rank].items():
if rank in median_rel_dist:
delta = dist - median_rel_dist[rank]
closest_rank_dist = 1e10
for test_rank, test_median in median_rel_dist.items():
abs_dist = abs(dist - test_median)
if abs_dist < closest_rank_dist:
closest_rank_dist = abs_dist
closest_rank = Taxonomy.rank_labels[test_rank]
classification = "OK"
if delta < -0.2:
classification = "very overclassified"
elif delta < -0.1:
classification = "overclassified"
elif delta > 0.2:
classification = "very underclassified"
elif delta > 0.1:
classification = "underclassified"
fout.write('%s\t%s\t%.3f\t%.3f\t%s\t%s\n' % (clade_label,
';'.join(gtdb_parent_ranks[clade_label]),
dist,
delta,
closest_rank,
classification))
else:
fout.write('%s\t%s\t%.3f\t%.3f\t%s\t%s\n' % (clade_label,
';'.join(gtdb_parent_ranks[clade_label]),
dist,
-1,
'NA',
'Insufficent data to calcualte median for rank.'))
fout.close()
def _pairwise_stats(self, clusters, genome_files):
"""Calculate statistics for all pairwise comparisons in a species cluster."""
self.logger.info('Calculating statistics for all pairwise comparisons in a species cluster:')
stats = {}
for idx, (rid, cids) in enumerate(clusters.items()):
statusStr = '-> Processing %d of %d (%.2f%%) clusters (size = %d).'.ljust(86) % (
idx+1,
len(clusters),
float((idx+1)*100)/len(clusters),
len(cids))
sys.stdout.write('%s\r' % statusStr)
sys.stdout.flush()
if len(cids) == 0:
stats[rid] = self.PairwiseStats(min_ani = -1,
mean_ani = -1,
std_ani = -1,
median_ani = -1,
ani_to_medoid = -1,
mean_ani_to_medoid = -1,
ani_below_95 = -1)
else:
if len(cids) > self.max_genomes_for_stats:
cids = set(random.sample(cids, self.max_genomes_for_stats))
# calculate ANI to representative genome
gid_pairs = []
gids = list(cids.union([rid]))
for gid1, gid2 in combinations(gids, 2):
gid_pairs.append((gid1, gid2))
gid_pairs.append((gid2, gid1))
ani_af = self.ani_cache.fastani_pairs(gid_pairs,
genome_files,
report_progress=False)
# calculate medoid point
if len(gids) > 2:
dist_mat = np_zeros((len(gids), len(gids)))
for i, gid1 in enumerate(gids):
for j, gid2 in enumerate(gids):
if i < j:
ani, af = symmetric_ani(ani_af, gid1, gid2)
dist_mat[i, j] = ani
dist_mat[j, i] = ani
medoid_idx = np_argmin(dist_mat.sum(axis=0))
medoid_gid = gids[medoid_idx]
else:
# with only 2 genomes in a cluster, the representative is the
# natural medoid at least for reporting statistics for the
# individual species cluster
medoid_gid = rid
mean_ani_to_medoid = np_mean([symmetric_ani(ani_af, gid, medoid_gid)[0]
for gid in gids if gid != medoid_gid])
# calculate statistics
anis = []
for gid1, gid2 in combinations(gids, 2):
ani, af = symmetric_ani(ani_af, gid1, gid2)
anis.append(ani)
stats[rid] = self.PairwiseStats(min_ani = min(anis),
mean_ani = np_mean(anis),
std_ani = np_std(anis),
median_ani = np_median(anis),
ani_to_medoid = symmetric_ani(ani_af, rid, medoid_gid)[0],
mean_ani_to_medoid = mean_ani_to_medoid,
ani_below_95 = sum([1 for ani in anis if ani < 95]))
sys.stdout.write('\n')
return stats
def _calculate_red_distances(self, input_tree, out_dir):
"""
Provide a taxonomy string to a user genome based on the reference genomes of the same clade.
If the clade contains multiple reference genomes we are comparing their taxonomies.
-If all reference genomes have the same taxonomy up to the 'closest rank' ,
the taxonomy string including the closest rank is returned.
-If **NOT** all reference genomes have the same taxonomy up to the 'closest rank',
the taxonomy string **NOT** including the closest rank is returned.
Parameters
----------
list_subnode : list of leaf nodes including multiple reference genome.
closest_rank : last rank of the reference taxonomy
gtdb_taxonomy : dictionary storing all the reference taxonomies
Returns
-------
string
Taxonomy string.
"""
# read tree
self.logger.info('Reading tree.')
tree = dendropy.Tree.get_from_path(input_tree,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
self.logger.info('Reading taxonomy from file.')
taxonomy = Taxonomy().read(Config.TAXONOMY_FILE)
# determine taxa to be used for inferring distribution
trusted_taxa = None
taxa_for_dist_inference = self._filter_taxa_for_dist_inference(
tree, taxonomy, trusted_taxa, Config.RED_MIN_CHILDREN,
Config.RED_MIN_SUPPORT)
phylum_rel_dists, rel_node_dists = self.median_rd_over_phyla(
tree, taxa_for_dist_inference, taxonomy)
# set edge lengths to median value over all rootings
tree.seed_node.rel_dist = 0.0
for n in tree.preorder_node_iter(lambda n: n != tree.seed_node):
n.rel_dist = np_median(rel_node_dists[n.id])
rd_to_parent = n.rel_dist - n.parent_node.rel_dist
if rd_to_parent < 0:
# This can occur since we are setting all nodes
# to their median RED value.
#self.logger.warning('Not all branches are positive after scaling.')
pass
n.edge_length = rd_to_parent
if False:
# These plots can be useful for debugging and internal use,
# but are likely to be confusing to users.
rd = RelativeDistance()
input_tree_name = os.path.splitext(os.path.basename(input_tree))[0]
plot_file = os.path.join(out_dir, '%s.png' % input_tree_name)
rd._distribution_summary_plot(phylum_rel_dists,
taxa_for_dist_inference, plot_file)
gtdb_parent_ranks = Taxonomy().parents(taxonomy)
median_outlier_table = os.path.join(out_dir,
'%s.tsv' % input_tree_name)
median_rank_file = os.path.join(out_dir,
'%s.dict' % input_tree_name)
rd._median_summary_outlier_file(phylum_rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table,
median_rank_file, False)
input_tree_name = os.path.splitext(os.path.basename(input_tree))[0]
output_tree = os.path.join(out_dir,
'%s.scaled.tree' % input_tree_name)
tree.write_to_path(output_tree,
schema='newick',
suppress_rooting=True,
unquoted_underscores=True)
return tree
def _distribution_summary_plot(self,
phylum_rel_dists,
taxa_for_dist_inference,
highlight_polyphyly,
highlight_taxa,
fmeasure,
fmeasure_mono,
plot_file):
"""Summary plot showing the distribution of taxa at each taxonomic rank under different rootings.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
plot_file : str
Desired name of output plot.
"""
self.fig.clear()
self.fig.set_size_inches(12, 6)
ax = self.fig.add_subplot(111)
# determine median relative distance for each taxa
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
# create percentile and classification boundary lines
percentiles = {}
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
v = [np_median(dists) for taxon, dists in medians_for_taxa[rank].iteritems() if taxon in taxa_for_dist_inference]
if not v:
# not taxa at rank suitable for creating classification boundaries
continue
p10, p50, p90 = np_percentile(v, [10, 50, 90])
#ax.plot((p10, p10), (i, i + 0.25), c=(0.3, 0.3, 0.3), lw=2, zorder=2)
ax.plot((p50, p50), (i, i + 0.5), c=(0.0, 0.0, 1.0), lw=2, zorder=2)
#ax.plot((p90, p90), (i, i + 0.25), c=(0.3, 0.3, 0.3), lw=2, zorder=2)
for b in [-0.1, 0.1]:
boundary = p50 + b
if boundary < 1.0 and boundary > 0.0:
if abs(b) == 0.1:
c = (0.0, 0.0, 0.0)
else:
c = (1.0, 0.0, 0.0)
ax.plot((boundary, boundary), (i, i + 0.5), c=c, lw=2, zorder=2)
percentiles[i] = [p10, p50, p90]
# create scatter plot and results table
x = []
y = []
c = []
labels = []
rank_labels = []
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
rank_label = Taxonomy.rank_labels[rank]
rank_labels.append(rank_label.capitalize() + ' (%d)' % len(medians_for_taxa[rank]))
mono = []
poly = []
near_mono = []
for clade_label, dists in medians_for_taxa[rank].iteritems():
md = np_median(dists)
x.append(md)
y.append(i)
labels.append(clade_label)
if ((highlight_polyphyly and fmeasure[clade_label] < fmeasure_mono) or clade_label in highlight_taxa):
c.append((1.0,0.0,0.0))
poly.append(md)
elif (highlight_polyphyly and fmeasure[clade_label] != 1.0):
c.append((255.0/255,187.0/255,120.0/255))
near_mono.append(md)
else:
c.append((152.0/255,223.0/255,138.0/255))
mono.append(md)
# histogram for each rank
binwidth = 0.025
bins = np_arange(0, 1.0 + binwidth, binwidth)
max_bin_count = max(np_histogram(mono + near_mono + poly, bins=bins)[0])
mono_bottom = 0
near_mono_bottom = 0
mono = np_array(mono)
near_mono = np_array(near_mono)
poly = np_array(poly)
if len(mono) > 0:
mono_bottom, b, p = ax.hist(mono, bins=bins,
color=(152.0/255,223.0/255,138.0/255),
alpha=0.5,
weights=0.9 * (1.0 / max_bin_count) * np_ones_like(mono),
bottom=i,
lw=0,
zorder=0)
if len(near_mono) > 0:
near_mono_bottom, b, p = ax.hist(near_mono, bins=bins,
color=(255.0/255,187.0/255,120.0/255),
alpha=0.5,
weights=0.9 * (1.0 / max_bin_count) * np_ones_like(near_mono),
bottom=i + mono_bottom,
lw=0,
zorder=0)
if len(poly) > 0:
ax.hist(poly, bins=bins,
color=(1.0, 0.0, 0.0),
alpha=0.5,
weights=0.9 * (1.0 / max_bin_count) * np_ones_like(poly),
bottom=i + mono_bottom + near_mono_bottom,
lw=0,
zorder=0)
scatter = ax.scatter(x, y, alpha=0.5, s=48, c=c, zorder=1)
# set plot elements
ax.grid(color=(0.8, 0.8, 0.8), linestyle='dashed')
ax.set_xlabel('Relative Evolutionary Divergence')
ax.set_xticks(np_arange(0, 1.05, 0.1))
ax.set_xlim([-0.01, 1.01])
ax.set_ylabel('Rank (no. taxa)')
ax.set_yticks(xrange(0, len(medians_for_taxa)))
ax.set_ylim([-0.2, len(medians_for_taxa) - 0.01])
ax.set_yticklabels(rank_labels)
self.prettify(ax)
# make plot interactive
mpld3.plugins.clear(self.fig)
mpld3.plugins.connect(self.fig, mpld3.plugins.PointLabelTooltip(scatter, labels=labels))
mpld3.plugins.connect(self.fig, mpld3.plugins.MousePosition(fontsize=10))
mpld3.save_html(self.fig, plot_file[0:plot_file.rfind('.')] + '.html')
self.fig.tight_layout(pad=1)
self.fig.savefig(plot_file, dpi=self.dpi)
self.fig.savefig(plot_file.replace('.png', '.svg'), dpi=self.dpi)
def _distribution_summary_plot(self, phylum_rel_dists, taxa_for_dist_inference, plot_file):
"""Summary plot showing the distribution of taxa at each taxonomic rank under different rootings.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
plot_file : str
Desired name of output plot.
"""
self.fig.clear()
self.fig.set_size_inches(12, 6)
ax = self.fig.add_subplot(111)
# determine median relative distance for each taxa
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
# create percentile and classification boundary lines
percentiles = {}
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
v = [np_median(dists) for taxon, dists in medians_for_taxa[rank].iteritems() if taxon in taxa_for_dist_inference]
p10, p50, p90 = np_percentile(v, [10, 50, 90])
ax.plot((p10, p10), (i, i + 0.25), c=(0.3, 0.3, 0.3), lw=2, zorder=2)
ax.plot((p50, p50), (i, i + 0.5), c=(0.3, 0.3, 0.3), lw=2, zorder=2)
ax.plot((p90, p90), (i, i + 0.25), c=(0.3, 0.3, 0.3), lw=2, zorder=2)
for b in [-0.2, -0.1, 0.1, 0.2]:
boundary = p50 + b
if boundary < 1.0 and boundary > 0.0:
if abs(b) == 0.1:
c = (1.0, 0.65, 0.0) # orange
else:
c = (1.0, 0.0, 0.0)
ax.plot((boundary, boundary), (i, i + 0.5), c=c, lw=2, zorder=2)
percentiles[i] = [p10, p50, p90]
# create scatter plot and results table
x = []
y = []
c = []
labels = []
rank_labels = []
for i, rank in enumerate(sorted(medians_for_taxa.keys())):
rank_label = Taxonomy.rank_labels[rank]
rank_labels.append(rank_label + ' (%d)' % len(medians_for_taxa[rank]))
mono = []
poly = []
no_inference = []
for clade_label, dists in medians_for_taxa[rank].iteritems():
md = np_median(dists)
x.append(md)
y.append(i)
labels.append(clade_label)
if is_integer(clade_label.split('^')[-1]):
# taxa with a numerical suffix after a caret indicate
# polyphyletic groups when decorated with tax2tree
c.append((1.0, 0.0, 0.0))
poly.append(md)
elif clade_label not in taxa_for_dist_inference:
c.append((0.3, 0.3, 0.3))
no_inference.append(md)
else:
c.append((0.0, 0.0, 1.0))
mono.append(md)
# histogram for each rank
mono = np_array(mono)
no_inference = np_array(no_inference)
poly = np_array(poly)
binwidth = 0.025
bins = np_arange(0, 1.0 + binwidth, binwidth)
mono_max_count = max(np_histogram(mono, bins=bins)[0])
mono_weights = np_ones_like(mono) * (1.0 / mono_max_count)
w = float(len(mono)) / (len(mono) + len(poly) + len(no_inference))
n, b, p = ax.hist(mono, bins=bins,
color=(0.0, 0.0, 1.0),
alpha=0.25,
weights=0.9 * w * mono_weights,
bottom=i,
lw=0,
zorder=0)
if len(no_inference) > 0:
no_inference_max_count = max(np_histogram(no_inference, bins=bins)[0])
no_inference_weights = np_ones_like(no_inference) * (1.0 / no_inference_max_count)
ax.hist(no_inference, bins=bins,
color=(0.3, 0.3, 0.3),
alpha=0.25,
weights=0.9 * (1.0 - w) * no_inference_weights,
bottom=i + n,
lw=0,
zorder=0)
if len(poly) > 0:
poly_max_count = max(np_histogram(poly, bins=bins)[0])
poly_weights = np_ones_like(poly) * (1.0 / poly_max_count)
ax.hist(poly, bins=bins,
color=(1.0, 0.0, 0.0),
alpha=0.25,
weights=0.9 * (1.0 - w) * poly_weights,
bottom=i + n,
lw=0,
zorder=0)
scatter = ax.scatter(x, y, alpha=0.5, s=48, c=c, zorder=1)
# set plot elements
ax.grid(color=(0.8, 0.8, 0.8), linestyle='dashed')
ax.set_xlabel('relative distance')
ax.set_xticks(np_arange(0, 1.05, 0.1))
ax.set_xlim([-0.01, 1.01])
ax.set_ylabel('rank (no. taxa)')
ax.set_yticks(xrange(0, len(medians_for_taxa)))
ax.set_ylim([-0.2, len(medians_for_taxa) - 0.01])
ax.set_yticklabels(rank_labels)
self.prettify(ax)
# make plot interactive
mpld3.plugins.clear(self.fig)
mpld3.plugins.connect(self.fig, mpld3.plugins.PointLabelTooltip(scatter, labels=labels))
mpld3.plugins.connect(self.fig, mpld3.plugins.MousePosition(fontsize=10))
mpld3.save_html(self.fig, plot_file[0:plot_file.rfind('.')] + '.html')
self.fig.tight_layout(pad=1)
self.fig.savefig(plot_file, dpi=self.dpi)
def run(self, input_tree,
taxonomy_file,
output_dir,
plot_taxa_file,
plot_dist_taxa_only,
plot_domain,
trusted_taxa_file,
fixed_root,
min_children,
min_support,
verbose_table):
"""Determine distribution of taxa at each taxonomic rank.
Parameters
----------
input_tree : str
Name of input tree.
taxonomy_file : str
File with taxonomy strings for each taxa.
output_dir : str
Desired output directory.
plot_taxa_file : str
File specifying taxa to plot. Set to None to consider all taxa.
plot_dist_taxa_only : boolean
Only plot the taxa used to infer distribution.
plot_domain : boolean
Plot domain rank.
trusted_taxa_file : str
File specifying trusted taxa to consider when inferring distribution. Set to None to consider all taxa.
fixed_root : boolean
Usa a single fixed root to infer outliers.
min_children : int
Only consider taxa with at least the specified number of children taxa when inferring distribution.
min_support : float
Only consider taxa with at least this level of support when inferring distribution.
verbose_table : boolean
Print additional columns in output table.
"""
# read tree
self.logger.info('Reading tree.')
tree = dendropy.Tree.get_from_path(input_tree,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
input_tree_name = os.path.splitext(os.path.basename(input_tree))[0]
# pull taxonomy from tree
if not taxonomy_file:
self.logger.info('Reading taxonomy from tree.')
taxonomy_file = os.path.join(output_dir, '%s.taxonomy.tsv' % input_tree_name)
taxonomy = Taxonomy().read_from_tree(input_tree)
Taxonomy().write(taxonomy, taxonomy_file)
else:
self.logger.info('Reading taxonomy from file.')
taxonomy = Taxonomy().read(taxonomy_file)
gtdb_parent_ranks = Taxonomy().parents(taxonomy)
# read trusted taxa
trusted_taxa = None
if trusted_taxa_file:
trusted_taxa = read_taxa_file(trusted_taxa_file)
# determine taxa to be used for inferring distribution
taxa_for_dist_inference = filter_taxa_for_dist_inference(tree, taxonomy, trusted_taxa, min_children, min_support)
# limit plotted taxa
taxa_to_plot = None
if plot_dist_taxa_only:
taxa_to_plot = taxa_for_dist_inference
elif plot_taxa_file:
taxa_to_plot = read_taxa_file(plot_taxa_file)
# check if a single fixed root should be used
if fixed_root:
self.logger.info('Using single fixed rooting for inferring distributions.')
rel_dists = self.rd_fixed_root(tree, taxa_for_dist_inference)
# create fixed rooting style tables and plots
distribution_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
plot_file = os.path.join(output_dir, '%s.png' % input_tree_name)
self._distribution_plot(rel_dists, taxa_for_dist_inference, distribution_table, plot_file)
median_outlier_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
self._median_outlier_file(rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table)
else:
# calculate relative distance to taxa
rd = RelativeDistance()
rel_dists = rd.rel_dist_to_named_clades(tree)
# report number of taxa at each rank
print ''
print 'Rank\tTaxa to Plot\tTaxa for Inference'
for rank, taxa in rel_dists.iteritems():
taxa_for_inference = [x for x in taxa if x in taxa_for_dist_inference]
print '%s\t%d\t%d' % (Taxonomy.rank_labels[rank], len(taxa), len(taxa_for_inference))
print ''
phylum_rel_dists, rel_node_dists = self.median_rd_over_phyla(tree,
taxa_for_dist_inference,
taxonomy)
# set edge lengths to median value over all rootings
tree.seed_node.rel_dist = 0.0
for n in tree.preorder_node_iter(lambda n: n != tree.seed_node):
n.rel_dist = np_median(rel_node_dists[n.id])
rd_to_parent = n.rel_dist - n.parent_node.rel_dist
if rd_to_parent < 0:
self.logger.warning('Not all branches are positive after scaling.')
n.edge_length = rd_to_parent
for phylum, rel_dists in phylum_rel_dists.iteritems():
phylum_dir = os.path.join(output_dir, phylum)
if not os.path.exists(phylum_dir):
os.makedirs(phylum_dir)
# create distribution plot
distribution_table = os.path.join(phylum_dir, '%s.rank_distribution.tsv' % phylum)
plot_file = os.path.join(phylum_dir, '%s.rank_distribution.png' % phylum)
self._distribution_plot(rel_dists, taxa_for_dist_inference, distribution_table, plot_file)
median_outlier_table = os.path.join(phylum_dir, '%s.median_outlier.tsv' % phylum)
self._median_outlier_file(rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table)
plot_file = os.path.join(output_dir, '%s.png' % input_tree_name)
self._distribution_summary_plot(phylum_rel_dists, taxa_for_dist_inference, plot_file)
median_outlier_table = os.path.join(output_dir, '%s.tsv' % input_tree_name)
median_rank_file = os.path.join(output_dir, '%s.dict' % input_tree_name)
self._median_summary_outlier_file(phylum_rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
median_outlier_table,
median_rank_file,
verbose_table)
output_tree = os.path.join(output_dir, '%s.scaled.tree' % input_tree_name)
tree.write_to_path(output_tree,
schema='newick',
suppress_rooting=True,
unquoted_underscores=True)
def _median_outlier_file(self,
rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
output_file):
"""Identify outliers relative to the median of rank distributions.
Parameters
----------
rel_dists: d[rank_index][taxon] -> relative divergence
Relative divergence of taxa at each rank.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
gtdb_parent_ranks: d[taxon] -> string indicating parent taxa
Parent taxa for each taxon.
output_file : str
Desired name of output table.
"""
# determine median relative distance for each rank
median_rel_dist = {}
for rank, d in rel_dists.iteritems():
v = [dist for taxa, dist in d.iteritems() if taxa in taxa_for_dist_inference]
if len(v) == 0:
continue
median_rel_dist[rank] = np_median(v)
fout = open(output_file, 'w')
fout.write('Taxa\tGTDB taxonomy\tMedian distance\tMean difference\tClosest rank\tClassification\n')
for i, rank in enumerate(sorted(rel_dists.keys())):
for clade_label, dist in rel_dists[rank].iteritems():
if rank in median_rel_dist:
delta = dist - median_rel_dist[rank]
closest_rank_dist = 1e10
for test_rank, test_median in median_rel_dist.iteritems():
abs_dist = abs(dist - test_median)
if abs_dist < closest_rank_dist:
closest_rank_dist = abs_dist
closest_rank = Taxonomy.rank_labels[test_rank]
classification = "OK"
if delta < -0.2:
classification = "very overclassified"
elif delta < -0.1:
classification = "overclassified"
elif delta > 0.2:
classification = "very underclassified"
elif delta > 0.1:
classification = "underclassified"
fout.write('%s\t%s\t%.3f\t%.3f\t%s\t%s\n' % (clade_label,
';'.join(gtdb_parent_ranks[clade_label]),
dist,
delta,
closest_rank,
classification))
else:
fout.write('%s\t%s\t%.3f\t%.3f\t%s\t%s\n' % (clade_label,
';'.join(gtdb_parent_ranks[clade_label]),
dist,
-1,
'NA',
'Insufficent data to calcualte median for rank.'))
fout.close()
def _median_summary_outlier_file(self, phylum_rel_dists,
taxa_for_dist_inference,
gtdb_parent_ranks,
outlier_table,
rank_file,
verbose_table):
"""Identify outliers relative to the median of rank distributions.
Parameters
----------
phylum_rel_dists: phylum_rel_dists[phylum][rank_index][taxon] -> relative divergences
Relative divergence of taxon at each rank for different phylum-level rootings.
taxa_for_dist_inference : iterable
Taxa to considered when inferring distributions.
gtdb_parent_ranks: d[taxon] -> string indicating parent taxa
Parent taxa for each taxon.
outlier_table : str
Desired name of output table.
rank_file : str
Desired name of file indicating median relative distance of each rank.
verbose_table : boolean
Print additional columns in output table.
"""
# determine median relative distance for each taxa
medians_for_taxa = self.taxa_median_rd(phylum_rel_dists)
# determine median relative distance for each rank
median_for_rank = self.rank_median_rd(phylum_rel_dists, taxa_for_dist_inference)
fout_rank = open(rank_file, 'w')
median_str = []
for rank in sorted(median_for_rank.keys()):
median_str.append('"' + Taxonomy.rank_labels[rank] + '":' + str(median_for_rank[rank]))
fout_rank.write('{' + ','.join(median_str) + '}\n')
fout_rank.close()
fout = open(outlier_table, 'w')
if verbose_table:
fout.write('Taxa\tGTDB taxonomy\tMedian distance')
fout.write('\tMedian of rank\tMedian difference')
fout.write('\tClosest rank\tClassifciation\n')
else:
fout.write('Taxa\tGTDB taxonomy\tMedian distance\tMedian difference\tClosest rank\tClassification\n')
for rank in sorted(median_for_rank.keys()):
for clade_label, dists in medians_for_taxa[rank].iteritems():
dists = np_array(dists)
taxon_median = np_median(dists)
delta = taxon_median - median_for_rank[rank]
closest_rank_dist = 1e10
for test_rank, test_median in median_for_rank.iteritems():
abs_dist = abs(taxon_median - test_median)
if abs_dist < closest_rank_dist:
closest_rank_dist = abs_dist
closest_rank = Taxonomy.rank_labels[test_rank]
classification = "OK"
if delta < -0.2:
classification = "very overclassified"
elif delta < -0.1:
classification = "overclassified"
elif delta > 0.2:
classification = "very underclassified"
elif delta > 0.1:
classification = "underclassified"
if verbose_table:
fout.write('%s\t%s\t%.2f\t%.3f\t%.3f\t%s\t%s\n' % (clade_label,
';'.join(gtdb_parent_ranks[clade_label]),
taxon_median,
median_for_rank[rank],
delta,
closest_rank,
classification))
else:
fout.write('%s\t%s\t%.3f\t%.3f\t%s\t%s\n' % (clade_label,
';'.join(gtdb_parent_ranks[clade_label]),
taxon_median,
delta,
closest_rank,
classification))
fout.close()
for i in orig_list3:
more, less = 0, 0
for j in orig_list3:
if i > j:
more += 1
elif i < j:
less += 1
if more == less:
median = i
break
print('Медиана:', median)
from numpy import median as np_median
print('Проверим по numpy:', np_median(orig_list3))
def gnome_sort(orig_list):
i = 1
while i < len(orig_list):
if not i or orig_list[i - 1] <= orig_list[i]:
i += 1
else:
orig_list[i], orig_list[i - 1] = orig_list[i - 1], orig_list[i]
i -= 1
return orig_list
print('Гномьей сортировкой по возрастанию:', gnome_sort(orig_list3))
print('m-й элемент:', gnome_sort(orig_list3)[m])
def create_feat_mat(graph_list, n_feats):
dens_pos = [nx_density(graph) for graph in graph_list]
nodes_pos = [nx_number_of_nodes(graph) for graph in graph_list]
# CC statistics - mean and max - faster to use a big loop mostly
CC_mean = []
CC_mean_append = CC_mean.append
CC_max = []
CC_max_append = CC_max.append
CC_var = []
CC_var_append = CC_var.append
# Degree correlation - avg degree of the neighborhood
DC_mean = []
DC_mean_append = DC_mean.append
DC_max = []
DC_max_append = DC_max.append
DC_var = []
DC_var_append = DC_var.append
# Degree statistics
degree_mean = []
degree_mean_append = degree_mean.append
degree_max = []
degree_max_append = degree_max.append
degree_median = []
degree_median_append = degree_median.append
degree_var = []
degree_var_append = degree_var.append
# Edge weight statistics
edge_wt_mean = []
edge_wt_mean_append = edge_wt_mean.append
edge_wt_max = []
edge_wt_max_append = edge_wt_max.append
edge_wt_var = []
edge_wt_var_append = edge_wt_var.append
# First 3 singular values
sv1 = []
sv1_append = sv1.append
sv2 = []
sv2_append = sv2.append
sv3 = []
sv3_append = sv3.append
for graph in graph_list:
CCs = list(nx_clustering(graph).values())
CC_max_append(max(CCs))
CC_mean_append(np_mean(CCs))
CC_var_append(np_var(CCs))
DCs = list(nx_average_neighbor_degree(graph).values())
DC_max_append(max(DCs))
DC_mean_append(np_mean(DCs))
DC_var_append(np_var(DCs))
degrees = [tup[1] for tup in graph.degree()]
degree_mean_append(np_mean(degrees))
degree_median_append(np_median(degrees))
degree_max_append(max(degrees))
degree_var_append(np_var(degrees))
edge_wts = [tup[2] for tup in graph.edges.data('weight')]
edge_wt_mean_append(np_mean(edge_wts))
edge_wt_var_append(np_var(edge_wts))
edge_wt_max_append(max(edge_wts))
A_mat = nx_to_numpy_matrix(graph)
svs = np_linalg_svd(A_mat, full_matrices=False, compute_uv=False)
if len(svs) >= 3:
sv1_append(svs[0])
sv2_append(svs[1])
sv3_append(svs[2])
elif len(svs) >= 2:
sv1_append(svs[0])
sv2_append(svs[1])
sv3_append(0)
else:
sv1_append(svs[0])
sv2_append(0)
sv3_append(0)
feat_mat = np_vstack((dens_pos, nodes_pos, degree_max, degree_mean, degree_median, degree_var, CC_max, CC_mean,
CC_var, edge_wt_mean, edge_wt_max, edge_wt_var, DC_mean, DC_var, DC_max, sv1, sv2, sv3)).T
if n_feats == 1:
feat_mat = np_array(dens_pos).reshape(-1, 1)
return feat_mat