def qa(self, options):
"""QA command"""
self.logger.info('[CheckM - qa] Tabulating genome statistics.')
checkDirExists(options.analyze_dir)
if options.exclude_markers:
checkFileExists(options.exclude_markers)
# calculate AAI between marks with multiple hits in a single bin
aai = AminoAcidIdentity()
aai.run(options.aai_strain, options.analyze_dir,
options.alignment_file)
# get HMM file for each bin
markerSetParser = MarkerSetParser(options.threads)
hmmModelInfoFile = os.path.join(options.analyze_dir, 'storage',
DefaultValues.CHECKM_HMM_MODEL_INFO)
binIdToModels = markerSetParser.loadBinModels(hmmModelInfoFile)
binIdToBinMarkerSets = markerSetParser.getMarkerSets(
options.analyze_dir, getBinIdsFromOutDir(options.analyze_dir),
options.marker_file, options.exclude_markers)
# get results for each bin
RP = ResultsParser(binIdToModels)
RP.analyseResults(
options.analyze_dir,
DefaultValues.BIN_STATS_OUT,
DefaultValues.HMMER_TABLE_OUT,
bIgnoreThresholds=options.bIgnoreThresholds,
evalueThreshold=options.e_value,
lengthThreshold=options.length,
bSkipPseudoGeneCorrection=options.bSkipPseudoGeneCorrection,
bSkipAdjCorrection=options.bSkipAdjCorrection)
RP.printSummary(options.out_format,
aai,
binIdToBinMarkerSets,
options.bIndividualMarkers,
options.coverage_file,
options.bTabTable,
options.file,
anaFolder=options.analyze_dir)
RP.cacheResults(options.analyze_dir, binIdToBinMarkerSets,
options.bIndividualMarkers)
if options.file != '':
self.logger.info('QA information written to: ' + options.file)
self.timeKeeper.printTimeStamp()
def testMultiCopyStrainHetero(self):
"""Verify computation of strain heterogeneity score when there are multiple copies of a sequence."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95, 0.95, 0.95], 'g2': [0.1, 0.1, 0.1], 'g3': [0.95, 0.1, 0.1]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0 / 3.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 4.0 * 100 / 9.0)
def testMixedStrainHetero(self):
"""Verify computation of strain heterogeneity score on sequences with variable similarity."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.1], 'g3': [0.1]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 0.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 1.0 * 100 / 3.0)
def testAllStrainHetero(self):
"""Verify computation of strain heterogeneity score on highly similar sequences."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.95], 'g3': [0.95]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 100.0)
def testAllStrainHetero(self):
"""Verify computation of strain heterogeneity score on highly similar sequences."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.95], 'g3': [0.95]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 100.0)
def testMixedStrainHetero(self):
"""Verify computation of strain heterogeneity score on sequences with variable similarity."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.1], 'g3': [0.1]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 0.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 1.0 * 100 / 3.0)
def testMultiCopyStrainHetero(self):
"""Verify computation of strain heterogeneity score when there are multiple copies of a sequence."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {
'g1': [0.95, 0.95, 0.95],
'g2': [0.1, 0.1, 0.1],
'g3': [0.95, 0.1, 0.1]
}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0 / 3.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 4.0 * 100 / 9.0)
def binQAPlot(self, options):
"""Bin QA plot command"""
self.logger.info(
'[CheckM - bin_qa_plot] Creating bar plot of bin quality.')
checkDirExists(options.bin_dir)
makeSurePathExists(options.output_dir)
binFiles = self.binFiles(options.bin_dir, options.extension)
# read model info
# hmmModelInfoFile = os.path.join(options.analyze_dir, 'storage', DefaultValues.CHECKM_HMM_MODEL_INFO)
# binIdToModels = markerSetParser.loadBinModels(hmmModelInfoFile)
# read sequence stats file
resultsParser = ResultsParser(None)
binStatsExt = resultsParser.parseBinStatsExt(options.results_dir)
# create plot for each bin
plot = BinQAPlot(options)
bMakePlot = True
if not options.bIgnoreHetero:
aai = AminoAcidIdentity()
aai.run(options.aai_strain, options.results_dir, None)
bMakePlot = plot.plot(binFiles, binStatsExt, options.bIgnoreHetero,
aai.aaiHetero)
else:
bMakePlot = plot.plot(binFiles, binStatsExt, options.bIgnoreHetero,
None)
if bMakePlot:
outputFile = os.path.join(options.output_dir,
'bin_qa_plot.' + options.image_type)
plot.savePlot(outputFile, dpi=options.dpi)
self.logger.info('Plot written to: ' + outputFile)
self.timeKeeper.printTimeStamp()
def testDiffSeqs(self):
"""Verify computation of AAI on two completely different sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT', 'TGCA')
self.assertAlmostEqual(score, 0.0)
def testIdenticalInsertionSeqs(self):
"""Verify computation of AAI on two identical sequences with multiple insertions."""
aai = AminoAcidIdentity()
score = aai.aai('A-C-G-T', 'A-C-G-T')
self.assertAlmostEqual(score, 1.0)
def testDiffInsertionSeqs(self):
"""Verify computation of AAI on two different sequences with multiple insertions."""
aai = AminoAcidIdentity()
score = aai.aai('A-C-G-T', 'AACCGGT')
self.assertAlmostEqual(score, 4.0 / 7.0)
def testIncompleteSeqs(self):
"""Verify computation of AAI on incomplete sequence."""
aai = AminoAcidIdentity()
score = aai.aai('AAAACGTTTT', '---ACGG---')
self.assertAlmostEqual(score, 3.0 / 4.0)
def testSimilarSeqs(self):
"""Verify computation of AAI on two similar sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT', 'ACGG')
self.assertAlmostEqual(score, 3.0 / 4.0)
def testNonOverlappingSeqs(self):
"""Verify computation of AAI on two non-overlapping sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT----', '----TGCA')
self.assertAlmostEqual(score, 0.0)
def testPartialOverlappingSeqs(self):
"""Verify computation of AAI on two partially overlapping sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT--', '--GTAC')
self.assertAlmostEqual(score, 1.0)
def testIdentiticalSeqs(self):
"""Verify computation of AAI on identical sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT', 'ACGT')
self.assertAlmostEqual(score, 1.0)
def testDiffSeqs(self):
"""Verify computation of AAI on two completely different sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT', 'TGCA')
self.assertAlmostEqual(score, 0.0)
def testPartialOverlappingSeqs(self):
"""Verify computation of AAI on two partially overlapping sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT--', '--GTAC')
self.assertAlmostEqual(score, 1.0)
def testNonOverlappingSeqs(self):
"""Verify computation of AAI on two non-overlapping sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT----', '----TGCA')
self.assertAlmostEqual(score, 0.0)
def testIdentiticalSeqs(self):
"""Verify computation of AAI on identical sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT', 'ACGT')
self.assertAlmostEqual(score, 1.0)
def testDiffInsertionSeqs(self):
"""Verify computation of AAI on two different sequences with multiple insertions."""
aai = AminoAcidIdentity()
score = aai.aai('A-C-G-T', 'AACCGGT')
self.assertAlmostEqual(score, 4.0 / 7.0)
def testIdenticalInsertionSeqs(self):
"""Verify computation of AAI on two identical sequences with multiple insertions."""
aai = AminoAcidIdentity()
score = aai.aai('A-C-G-T', 'A-C-G-T')
self.assertAlmostEqual(score, 1.0)
def testSimilarSeqs(self):
"""Verify computation of AAI on two similar sequences."""
aai = AminoAcidIdentity()
score = aai.aai('ACGT', 'ACGG')
self.assertAlmostEqual(score, 3.0 / 4.0)
def testIncompleteSeqs(self):
"""Verify computation of AAI on incomplete sequence."""
aai = AminoAcidIdentity()
score = aai.aai('AAAACGTTTT', '---ACGG---')
self.assertAlmostEqual(score, 3.0 / 4.0)
