def testDistanceZero(self):
"""Verify computation of distances between genomic signatures."""
gs = GenomicSignatures(K = 2, threads = 1)
sig1 = gs.seqSignature('AACC')
sig2 = gs.seqSignature('AACC')
dist = gs.distance(sig1, sig2)
self.assertEqual(dist, 0)
def testDistanceMax(self):
"""Verify computation of distances between genomic signatures."""
gs = GenomicSignatures(K = 2, threads = 1)
sig1 = gs.seqSignature('AAAA')
sig2 = gs.seqSignature('GGGG')
dist = gs.distance(sig1, sig2)
self.assertAlmostEqual(dist, 2.0)
def testGenomicSignature(self):
"""Verify computation of genomic signature."""
gs = GenomicSignatures(K=2, threads=1)
sig = gs.seqSignature('AACC')
kmerOrder = gs.canonicalKmerOrder()
aaIndex = kmerOrder.index('AA')
acIndex = kmerOrder.index('AC')
ccIndex = kmerOrder.index('AC')
atIndex = kmerOrder.index('AT')
self.assertEqual(sig[aaIndex], 1.0 / 3.0)
self.assertEqual(sig[acIndex], 1.0 / 3.0)
self.assertEqual(sig[ccIndex], 1.0 / 3.0)
self.assertEqual(sig[atIndex], 0)
def testGenomicSignature(self):
"""Verify computation of genomic signature."""
gs = GenomicSignatures(K = 2, threads = 1)
sig = gs.seqSignature('AACC')
kmerOrder = gs.canonicalKmerOrder()
aaIndex = kmerOrder.index('AA')
acIndex = kmerOrder.index('AC')
ccIndex = kmerOrder.index('AC')
atIndex = kmerOrder.index('AT')
self.assertEqual(sig[aaIndex], 1.0/3.0)
self.assertEqual(sig[acIndex], 1.0/3.0)
self.assertEqual(sig[ccIndex], 1.0/3.0)
self.assertEqual(sig[atIndex], 0)
def __calculateResults(self, windowSizes, numWindows, genomeDir, queueIn, queueOut):
while True:
genomeId = queueIn.get(block=True, timeout=None)
if genomeId == None:
break
start = time.time()
seqs = readGenomicSeqsFromFasta(os.path.join(genomeDir, genomeId, genomeId + '.fna'))
genomeScaffold = 'NNNN'.join(seqs.values())
# calculate tetranucleotide signature of genome
gsCalculator = GenomicSignatures(4)
genomeSig = gsCalculator.seqSignature(genomeScaffold)
fout = open('./deltaTD/' + genomeId + '.tsv', 'w')
fout.write('# Tetra signature = ' + str(genomeSig) + '\n')
fout.close()
sys.exit()
# calculate tetranucleotide distance distribution for different window sizes
startW = time.time()
for windowSize in windowSizes:
endWindowPos = len(genomeScaffold) - windowSize
if endWindowPos <= 0:
# This might occur for the largest window sizes and smallest genomes
break
deltaTDs = []
while len(deltaTDs) != numWindows:
# pick random window
startWindow = randint(0, endWindowPos)
windowSig = gsCalculator.seqSignature(genomeScaffold[startWindow:(startWindow+windowSize)])
dist = gsCalculator.distance(genomeSig, windowSig)
deltaTDs.append(dist)
fout.write('Windows Size = ' + str(windowSize) + '\n')
fout.write(','.join(map(str, deltaTDs)) + '\n')
fout.close()
endW = time.time()
print(endW - startW)
queueOut.put(genomeId)
end = time.time()
print(end - start)
def __calculateResults(self, windowSizes, numWindows, genomeDir, queueIn, queueOut):
while True:
genomeId = queueIn.get(block=True, timeout=None)
if genomeId == None:
break
start = time.time()
seqs = readGenomicSeqsFromFasta(os.path.join(genomeDir, genomeId, genomeId + '.fna'))
genomeScaffold = 'NNNN'.join(seqs.values())
# calculate tetranucleotide signature of genome
gsCalculator = GenomicSignatures(4)
genomeSig = gsCalculator.seqSignature(genomeScaffold)
fout = open('./deltaTD/' + genomeId + '.tsv', 'w')
fout.write('# Tetra signature = ' + str(genomeSig) + '\n')
fout.close()
sys.exit()
# calculate tetranucleotide distance distribution for different window sizes
startW = time.time()
for windowSize in windowSizes:
endWindowPos = len(genomeScaffold) - windowSize
if endWindowPos <= 0:
# This might occur for the largest window sizes and smallest genomes
break
deltaTDs = []
while len(deltaTDs) != numWindows:
# pick random window
startWindow = randint(0, endWindowPos)
windowSig = gsCalculator.seqSignature(genomeScaffold[startWindow:(startWindow+windowSize)])
dist = gsCalculator.distance(genomeSig, windowSig)
deltaTDs.append(dist)
fout.write('Windows Size = ' + str(windowSize) + '\n')
fout.write(','.join(map(str, deltaTDs)) + '\n')
fout.close()
endW = time.time()
print endW - startW
queueOut.put(genomeId)
end = time.time()
print end - start
def tetraSignatures(self, options):
"""Tetranucleotide signature command"""
self.logger.info(
'[CheckM - tetra] Calculating tetranucleotide signature of sequences.'
)
checkFileExists(options.seq_file)
makeSurePathExists(os.path.dirname(options.output_file))
tetraSig = GenomicSignatures(4, options.threads)
tetraSig.calculate(options.seq_file, options.output_file)
self.logger.info('Tetranucletoide signatures written to: ' +
options.output_file)
self.timeKeeper.printTimeStamp()
def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist,
axesDeltaTD):
# Read reference distributions from file
dist = readDistribution('td_dist')
# get tetranucleotide signature for bin
seqs = readFasta(fastaFile)
binTools = BinTools()
binSig = binTools.binTetraSig(seqs, tetraSigs)
# get tetranucleotide distances for windows
genomicSig = GenomicSignatures(K=4, threads=1)
data = []
seqLens = []
deltaTDs = []
for seqId, seq in seqs.iteritems():
start = 0
end = self.options.td_window_size
seqLen = len(seq)
seqLens.append(seqLen)
deltaTDs.append(genomicSig.distance(tetraSigs[seqId], binSig))
while (end < seqLen):
windowSig = genomicSig.seqSignature(seq[start:end])
data.append(genomicSig.distance(windowSig, binSig))
start = end
end += self.options.td_window_size
if len(data) == 0:
axesHist.set_xlabel(
'[Error] No seqs >= %d, the specified window size' %
self.options.td_window_size)
return
deltaTDs = np.array(deltaTDs)
# Histogram plot
bins = [0.0]
binWidth = self.options.td_bin_width
binEnd = binWidth
while binEnd <= 1.0:
bins.append(binEnd)
binEnd += binWidth
axesHist.hist(data, bins=bins, normed=True, color=(0.5, 0.5, 0.5))
axesHist.set_xlabel(r'$\Delta$ TD')
axesHist.set_ylabel('% windows (' + str(self.options.td_window_size) +
' bp)')
# Prettify plot
for a in axesHist.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axesHist.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axesHist.yaxis.get_ticklines():
line.set_color(self.axesColour)
for line in axesHist.xaxis.get_ticklines():
line.set_color(self.axesColour)
for loc, spine in axesHist.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(self.axesColour)
# get CD bin statistics
meanTD, deltaTDs = binTools.tetraDiffDist(seqs, genomicSig, tetraSigs,
binSig)
# Delta-TD vs Sequence length plot
axesDeltaTD.scatter(deltaTDs,
seqLens,
c=abs(deltaTDs),
s=10,
lw=0.5,
cmap='gray_r')
axesDeltaTD.set_xlabel(r'$\Delta$ TD (mean TD = %.2f)' % meanTD)
axesDeltaTD.set_ylabel('Sequence length (kbp)')
_, yMaxSeqs = axesDeltaTD.get_ylim()
xMinSeqs, xMaxSeqs = axesDeltaTD.get_xlim()
# plot reference distributions
for distToPlot in distributionsToPlot:
boundKey = findNearest(dist[dist.keys()[0]].keys(), distToPlot)
x = []
y = []
for windowSize in dist:
x.append(dist[windowSize][boundKey])
y.append(windowSize)
# sort by y-values
sortIndexY = np.argsort(y)
x = np.array(x)[sortIndexY]
y = np.array(y)[sortIndexY]
# make sure x-values are strictly decreasing as y increases
# as this is conservative and visually satisfying
for i in xrange(0, len(x) - 1):
for j in xrange(i + 1, len(x)):
if x[j] > x[i]:
if j == len(x) - 1:
x[j] = x[i]
else:
x[j] = (x[j - 1] + x[j + 1]
) / 2 # interpolate values from neighbours
if x[j] > x[i]:
x[j] = x[i]
axesDeltaTD.plot(x, y, 'r--', lw=0.5, zorder=0)
# ensure y-axis include zero and covers all sequences
axesDeltaTD.set_ylim([0, yMaxSeqs])
# ensure x-axis is set appropriately for sequences
axesDeltaTD.set_xlim([xMinSeqs, xMaxSeqs])
# draw vertical line at x=0
axesDeltaTD.vlines(0,
0,
yMaxSeqs,
linestyle='dashed',
color=self.axesColour,
zorder=0)
# Change sequence lengths from bp to kbp
yticks = axesDeltaTD.get_yticks()
kbpLabels = []
for seqLen in yticks:
label = '%.1f' % (float(seqLen) / 1000)
label = label.replace('.0', '') # remove trailing zero
kbpLabels.append(label)
axesDeltaTD.set_yticklabels(kbpLabels)
# Prettify plot
for a in axesDeltaTD.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axesDeltaTD.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axesDeltaTD.yaxis.get_ticklines():
line.set_color(self.axesColour)
for line in axesDeltaTD.xaxis.get_ticklines():
line.set_color(self.axesColour)
for loc, spine in axesDeltaTD.spines.iteritems():
if loc in ['right', 'top']:
spine.set_color('none')
else:
spine.set_color(self.axesColour)
def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDeltaTD):
# Read reference distributions from file
dist = readDistribution("td_dist")
# get tetranucleotide signature for bin
seqs = readFasta(fastaFile)
binTools = BinTools()
binSig = binTools.binTetraSig(seqs, tetraSigs)
# get tetranucleotide distances for windows
genomicSig = GenomicSignatures(K=4, threads=1)
data = []
seqLens = []
deltaTDs = []
for seqId, seq in seqs.iteritems():
start = 0
end = self.options.td_window_size
seqLen = len(seq)
seqLens.append(seqLen)
deltaTDs.append(genomicSig.distance(tetraSigs[seqId], binSig))
while end < seqLen:
windowSig = genomicSig.seqSignature(seq[start:end])
data.append(genomicSig.distance(windowSig, binSig))
start = end
end += self.options.td_window_size
if len(data) == 0:
axesHist.set_xlabel("[Error] No seqs >= %d, the specified window size" % self.options.td_window_size)
return
deltaTDs = np.array(deltaTDs)
# Histogram plot
bins = [0.0]
binWidth = self.options.td_bin_width
binEnd = binWidth
while binEnd <= 1.0:
bins.append(binEnd)
binEnd += binWidth
axesHist.hist(data, bins=bins, normed=True, color=(0.5, 0.5, 0.5))
axesHist.set_xlabel(r"$\Delta$ TD")
axesHist.set_ylabel("% windows (" + str(self.options.td_window_size) + " bp)")
# Prettify plot
for a in axesHist.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axesHist.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axesHist.yaxis.get_ticklines():
line.set_color(self.axesColour)
for line in axesHist.xaxis.get_ticklines():
line.set_color(self.axesColour)
for loc, spine in axesHist.spines.iteritems():
if loc in ["right", "top"]:
spine.set_color("none")
else:
spine.set_color(self.axesColour)
# get CD bin statistics
meanTD, deltaTDs = binTools.tetraDiffDist(seqs, genomicSig, tetraSigs, binSig)
# Delta-TD vs Sequence length plot
axesDeltaTD.scatter(deltaTDs, seqLens, c=abs(deltaTDs), s=10, lw=0.5, cmap="gray_r")
axesDeltaTD.set_xlabel(r"$\Delta$ TD (mean TD = %.2f)" % meanTD)
axesDeltaTD.set_ylabel("Sequence length (kbp)")
_, yMaxSeqs = axesDeltaTD.get_ylim()
xMinSeqs, xMaxSeqs = axesDeltaTD.get_xlim()
# plot reference distributions
for distToPlot in distributionsToPlot:
boundKey = findNearest(dist[dist.keys()[0]].keys(), distToPlot)
x = []
y = []
for windowSize in dist:
x.append(dist[windowSize][boundKey])
y.append(windowSize)
# sort by y-values
sortIndexY = np.argsort(y)
x = np.array(x)[sortIndexY]
y = np.array(y)[sortIndexY]
# make sure x-values are strictly decreasing as y increases
# as this is conservative and visually satisfying
for i in xrange(0, len(x) - 1):
for j in xrange(i + 1, len(x)):
if x[j] > x[i]:
if j == len(x) - 1:
x[j] = x[i]
else:
x[j] = (x[j - 1] + x[j + 1]) / 2 # interpolate values from neighbours
if x[j] > x[i]:
x[j] = x[i]
axesDeltaTD.plot(x, y, "r--", lw=0.5, zorder=0)
# ensure y-axis include zero and covers all sequences
axesDeltaTD.set_ylim([0, yMaxSeqs])
# ensure x-axis is set appropriately for sequences
axesDeltaTD.set_xlim([xMinSeqs, xMaxSeqs])
# draw vertical line at x=0
axesDeltaTD.vlines(0, 0, yMaxSeqs, linestyle="dashed", color=self.axesColour, zorder=0)
# Change sequence lengths from bp to kbp
yticks = axesDeltaTD.get_yticks()
kbpLabels = []
for seqLen in yticks:
label = "%.1f" % (float(seqLen) / 1000)
label = label.replace(".0", "") # remove trailing zero
kbpLabels.append(label)
axesDeltaTD.set_yticklabels(kbpLabels)
# Prettify plot
for a in axesDeltaTD.yaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for a in axesDeltaTD.xaxis.majorTicks:
a.tick1On = True
a.tick2On = False
for line in axesDeltaTD.yaxis.get_ticklines():
line.set_color(self.axesColour)
for line in axesDeltaTD.xaxis.get_ticklines():
line.set_color(self.axesColour)
for loc, spine in axesDeltaTD.spines.iteritems():
if loc in ["right", "top"]:
spine.set_color("none")
else:
spine.set_color(self.axesColour)
def identifyOutliers(self, outDir, binFiles, tetraProfileFile,
distribution, reportType, outputFile):
"""Identify sequences that are outliers."""
self.logger.info('Reading reference distributions.')
gcBounds = readDistribution('gc_dist')
cdBounds = readDistribution('cd_dist')
tdBounds = readDistribution('td_dist')
fout = open(outputFile, 'w')
fout.write(
'Bin Id\tSequence Id\tSequence length\tOutlying distributions')
fout.write(
'\tSequence GC\tMean bin GC\tLower GC bound (%s%%)\tUpper GC bound (%s%%)'
% (distribution, distribution))
fout.write('\tSequence CD\tMean bin CD\tLower CD bound (%s%%)' %
distribution)
fout.write('\tSequence TD\tMean bin TD\tUpper TD bound (%s%%)\n' %
distribution)
processedBins = 0
for binFile in binFiles:
binId = binIdFromFilename(binFile)
processedBins += 1
self.logger.info('Finding outliers in %s (%d of %d).' %
(binId, processedBins, len(binFiles)))
seqs = readFasta(binFile)
meanGC, deltaGCs, seqGC = self.gcDist(seqs)
genomicSig = GenomicSignatures(K=4, threads=1)
tetraSigs = genomicSig.read(tetraProfileFile)
binSig = self.binTetraSig(seqs, tetraSigs)
meanTD, deltaTDs = self.tetraDiffDist(seqs, genomicSig, tetraSigs,
binSig)
gffFile = os.path.join(outDir, 'bins', binId,
DefaultValues.PRODIGAL_GFF)
if not os.path.exists(gffFile):
self.logger.error(
'Missing gene feature file (%s). This plot if not compatible with the --genes option.\n'
% DefaultValues.PRODIGAL_GFF)
sys.exit(1)
prodigalParser = ProdigalGeneFeatureParser(gffFile)
meanCD, deltaCDs, CDs = self.codingDensityDist(
seqs, prodigalParser)
# find keys into GC and CD distributions
closestGC = findNearest(np.array(list(gcBounds.keys())), meanGC)
sampleSeqLen = list(gcBounds[closestGC].keys())[0]
d = gcBounds[closestGC][sampleSeqLen]
gcLowerBoundKey = findNearest(list(d.keys()),
(100 - distribution) / 2.0)
gcUpperBoundKey = findNearest(list(d.keys()),
(100 + distribution) / 2.0)
closestCD = findNearest(np.array(list(cdBounds.keys())), meanCD)
sampleSeqLen = list(cdBounds[closestCD].keys())[0]
d = cdBounds[closestCD][sampleSeqLen]
cdLowerBoundKey = findNearest(list(d.keys()),
(100 - distribution) / 2.0)
tdBoundKey = findNearest(
list(tdBounds[list(tdBounds.keys())[0]].keys()), distribution)
index = 0
for seqId, seq in seqs.items():
seqLen = len(seq)
# find GC, CD, and TD bounds
closestSeqLen = findNearest(list(gcBounds[closestGC].keys()),
seqLen)
gcLowerBound = gcBounds[closestGC][closestSeqLen][
gcLowerBoundKey]
gcUpperBound = gcBounds[closestGC][closestSeqLen][
gcUpperBoundKey]
closestSeqLen = findNearest(list(cdBounds[closestCD].keys()),
seqLen)
cdLowerBound = cdBounds[closestCD][closestSeqLen][
cdLowerBoundKey]
closestSeqLen = findNearest(list(tdBounds.keys()), seqLen)
tdBound = tdBounds[closestSeqLen][tdBoundKey]
outlyingDists = []
if deltaGCs[index] < gcLowerBound or deltaGCs[
index] > gcUpperBound:
outlyingDists.append('GC')
if deltaCDs[index] < cdLowerBound:
outlyingDists.append('CD')
if deltaTDs[index] > tdBound:
outlyingDists.append('TD')
if (reportType == 'any' and len(outlyingDists) >= 1) or (
reportType == 'all' and len(outlyingDists) == 3):
fout.write(binId + '\t' + seqId + '\t%d' % len(seq) +
'\t' + ','.join(outlyingDists))
fout.write('\t%.1f\t%.1f\t%.1f\t%.1f' %
(seqGC[index] * 100, meanGC * 100,
(meanGC + gcLowerBound) * 100,
(meanGC + gcUpperBound) * 100))
fout.write('\t%.1f\t%.1f\t%.1f' %
(CDs[index] * 100, meanCD * 100,
(meanCD + cdLowerBound) * 100))
fout.write('\t%.3f\t%.3f\t%.3f' %
(deltaTDs[index], meanTD, tdBound) + '\n')
index += 1
fout.close()
def identifyOutliers(self, outDir, binFiles, tetraProfileFile, distribution, reportType, outputFile):
"""Identify sequences that are outliers."""
self.logger.info(' Reading reference distributions.')
gcBounds = readDistribution('gc_dist')
cdBounds = readDistribution('cd_dist')
tdBounds = readDistribution('td_dist')
fout = open(outputFile, 'w')
fout.write('Bin Id\tSequence Id\tSequence length\tOutlying distributions')
fout.write('\tSequence GC\tMean bin GC\tLower GC bound (%s%%)\tUpper GC bound (%s%%)' % (distribution, distribution))
fout.write('\tSequence CD\tMean bin CD\tLower CD bound (%s%%)' % distribution)
fout.write('\tSequence TD\tMean bin TD\tUpper TD bound (%s%%)\n' % distribution)
self.logger.info('')
processedBins = 0
for binFile in binFiles:
binId = binIdFromFilename(binFile)
processedBins += 1
self.logger.info(' Finding outliers in %s (%d of %d).' % (binId, processedBins, len(binFiles)))
seqs = readFasta(binFile)
meanGC, deltaGCs, seqGC = self.gcDist(seqs)
genomicSig = GenomicSignatures(K=4, threads=1)
tetraSigs = genomicSig.read(tetraProfileFile)
binSig = self.binTetraSig(seqs, tetraSigs)
meanTD, deltaTDs = self.tetraDiffDist(seqs, genomicSig, tetraSigs, binSig)
gffFile = os.path.join(outDir, 'bins', binId, DefaultValues.PRODIGAL_GFF)
if not os.path.exists(gffFile):
self.logger.error(' [Error] Missing gene feature file (%s). This plot if not compatible with the --genes option.\n' % DefaultValues.PRODIGAL_GFF)
sys.exit(1)
prodigalParser = ProdigalGeneFeatureParser(gffFile)
meanCD, deltaCDs, CDs = self.codingDensityDist(seqs, prodigalParser)
# find keys into GC and CD distributions
closestGC = findNearest(np.array(gcBounds.keys()), meanGC)
sampleSeqLen = gcBounds[closestGC].keys()[0]
d = gcBounds[closestGC][sampleSeqLen]
gcLowerBoundKey = findNearest(d.keys(), (100 - distribution) / 2.0)
gcUpperBoundKey = findNearest(d.keys(), (100 + distribution) / 2.0)
closestCD = findNearest(np.array(cdBounds.keys()), meanCD)
sampleSeqLen = cdBounds[closestCD].keys()[0]
d = cdBounds[closestCD][sampleSeqLen]
cdLowerBoundKey = findNearest(d.keys(), (100 - distribution) / 2.0)
tdBoundKey = findNearest(tdBounds[tdBounds.keys()[0]].keys(), distribution)
index = 0
for seqId, seq in seqs.iteritems():
seqLen = len(seq)
# find GC, CD, and TD bounds
closestSeqLen = findNearest(gcBounds[closestGC].keys(), seqLen)
gcLowerBound = gcBounds[closestGC][closestSeqLen][gcLowerBoundKey]
gcUpperBound = gcBounds[closestGC][closestSeqLen][gcUpperBoundKey]
closestSeqLen = findNearest(cdBounds[closestCD].keys(), seqLen)
cdLowerBound = cdBounds[closestCD][closestSeqLen][cdLowerBoundKey]
closestSeqLen = findNearest(tdBounds.keys(), seqLen)
tdBound = tdBounds[closestSeqLen][tdBoundKey]
outlyingDists = []
if deltaGCs[index] < gcLowerBound or deltaGCs[index] > gcUpperBound:
outlyingDists.append('GC')
if deltaCDs[index] < cdLowerBound:
outlyingDists.append('CD')
if deltaTDs[index] > tdBound:
outlyingDists.append('TD')
if (reportType == 'any' and len(outlyingDists) >= 1) or (reportType == 'all' and len(outlyingDists) == 3):
fout.write(binId + '\t' + seqId + '\t%d' % len(seq) + '\t' + ','.join(outlyingDists))
fout.write('\t%.1f\t%.1f\t%.1f\t%.1f' % (seqGC[index] * 100, meanGC * 100, (meanGC + gcLowerBound) * 100, (meanGC + gcUpperBound) * 100))
fout.write('\t%.1f\t%.1f\t%.1f' % (CDs[index] * 100, meanCD * 100, (meanCD + cdLowerBound) * 100))
fout.write('\t%.3f\t%.3f\t%.3f' % (deltaTDs[index], meanTD, tdBound) + '\n')
index += 1
fout.close()
