def tree(self, options):
"""Tree command"""
self.logger.info(
'[CheckM - tree] Placing bins in reference genome tree.')
binFiles = self.binFiles(options.bin_dir, options.extension)
if not options.bCalledGenes:
if not checkNuclotideSeqs(binFiles):
return
else:
if not checkProteinSeqs(binFiles):
return
# setup directory structure
makeSurePathExists(os.path.join(options.output_dir, 'bins'))
makeSurePathExists(os.path.join(options.output_dir, 'storage'))
# find phylogenetically informative genes in genome bins
mgf = MarkerGeneFinder(options.threads)
binIdToModels = mgf.find(binFiles, options.output_dir,
DefaultValues.HMMER_TABLE_PHYLO_OUT,
DefaultValues.HMMER_PHYLO_OUT,
DefaultValues.PHYLO_HMM_MODELS,
options.bKeepAlignment, options.bNucORFs,
options.bCalledGenes)
# write model information to file
markerSetParser = MarkerSetParser(options.threads)
hmmModelInfoFile = os.path.join(options.output_dir, 'storage',
DefaultValues.PHYLO_HMM_MODEL_INFO)
markerSetParser.writeBinModels(binIdToModels, hmmModelInfoFile)
# calculate statistics for each genome bin
binStats = BinStatistics(options.threads)
binStats.calculate(binFiles, options.output_dir,
DefaultValues.BIN_STATS_PHYLO_OUT)
# align identified marker genes
HA = HmmerAligner(options.threads)
resultsParser = HA.makeAlignmentToPhyloMarkers(
options.output_dir, DefaultValues.PHYLO_HMM_MODELS,
DefaultValues.HMMER_TABLE_PHYLO_OUT, binIdToModels, False,
DefaultValues.E_VAL, DefaultValues.LENGTH, False,
os.path.join(options.output_dir, 'storage', 'tree'))
# place bins into genome tree
pplacer = PplacerRunner(
threads=options.pplacer_threads
) # fix at one thread to keep memory requirements reasonable
pplacer.run(binFiles, resultsParser, options.output_dir,
options.bReducedTree)
self.timeKeeper.printTimeStamp()
def analyze(self, options, db=None):
"""Analyze command"""
self.logger.info(
'[CheckM - analyze] Identifying marker genes in bins.')
binFiles = self.binFiles(options.bin_dir, options.extension)
if not options.bCalledGenes:
if not checkNuclotideSeqs(binFiles):
return
else:
if not checkProteinSeqs(binFiles):
return
# setup directory structure
makeSurePathExists(options.output_dir)
makeSurePathExists(os.path.join(options.output_dir, 'bins'))
makeSurePathExists(os.path.join(options.output_dir, 'storage'))
makeSurePathExists(
os.path.join(options.output_dir, 'storage', 'aai_qa'))
# find marker genes in genome bins
mgf = MarkerGeneFinder(options.threads)
binIdToModels = mgf.find(binFiles, options.output_dir,
DefaultValues.HMMER_TABLE_OUT,
DefaultValues.HMMER_OUT, options.marker_file,
options.bKeepAlignment, options.bNucORFs,
options.bCalledGenes)
markerSetParser = MarkerSetParser(options.threads)
binIdToBinMarkerSets = markerSetParser.getMarkerSets(
options.output_dir, getBinIdsFromOutDir(options.output_dir),
options.marker_file)
hmmModelInfoFile = os.path.join(options.output_dir, 'storage',
DefaultValues.CHECKM_HMM_MODEL_INFO)
markerSetParser.writeBinModels(binIdToModels, hmmModelInfoFile)
self.timeKeeper.printTimeStamp()
# HMM model file
if markerSetParser.markerFileType(
options.marker_file) == BinMarkerSets.HMM_MODELS_SET:
markerFile = options.marker_file
else:
markerFile = DefaultValues.HMM_MODELS
# align marker genes with multiple hits within a bin
HA = HmmerAligner(options.threads)
HA.makeAlignmentsOfMultipleHits(
options.output_dir, markerFile, DefaultValues.HMMER_TABLE_OUT,
binIdToModels, binIdToBinMarkerSets, False, DefaultValues.E_VAL,
DefaultValues.LENGTH,
os.path.join(options.output_dir, 'storage', 'aai_qa'))
self.timeKeeper.printTimeStamp()
# calculate statistics for each genome bin
binStats = BinStatistics(options.threads)
binStats.calculate(binFiles, options.output_dir,
DefaultValues.BIN_STATS_OUT)
self.timeKeeper.printTimeStamp()
# align top hit to each marker if requested
if options.bAlignTopHit:
alignmentOutputFolder = os.path.join(options.output_dir, 'storage',
'alignments')
makeSurePathExists(alignmentOutputFolder)
HA = HmmerAligner(options.threads)
resultsParser = HA.makeAlignmentTopHit(
options.output_dir, options.marker_file,
DefaultValues.HMMER_TABLE_OUT, binIdToModels, False,
DefaultValues.E_VAL, DefaultValues.LENGTH, True,
alignmentOutputFolder)
# report marker gene data
fout = open(
os.path.join(alignmentOutputFolder, 'alignment_info.tsv'), 'w')
fout.write('Marker Id\tLength (bp)\n')
markerIds = resultsParser.models[list(
resultsParser.models.keys())[0]].keys()
for markerId in markerIds:
fout.write('%s\t%d\n' % (markerId, resultsParser.models[list(
resultsParser.models.keys())[0]][markerId].leng))
fout.close()
self.logger.info('Alignments to top hits stored in: ' +
alignmentOutputFolder)
self.timeKeeper.printTimeStamp()