def markerSet(self, rank, taxon, markerFile):
"""Obtain specified taxonomic-specific marker set."""
taxonMarkerSets = self.readMarkerSets()
if rank not in taxonMarkerSets:
self.logger.error(' Unrecognized taxonomic rank: ' + rank)
return False
elif taxon not in taxonMarkerSets[rank]:
self.logger.error(' Unrecognized taxon: %s (in rank %s): ' %
(taxon, rank))
return False
markerSet = taxonMarkerSets[rank][taxon]
taxonomy = markerSet.lineageStr.split(';')[::-1]
binMarkerSets = BinMarkerSets(taxon,
BinMarkerSets.TAXONOMIC_MARKER_SET)
for i, taxon in enumerate(taxonomy):
if rank != 'life':
rank = ranksByLevel[len(taxonomy) - i - 1]
if rank == 'species':
taxon = taxonomy[1] + ' ' + taxonomy[0]
markerSet = taxonMarkerSets[rank][taxon]
numMarkers, numMarkerSets = markerSet.size()
self.logger.info(
' Marker set for %s contains %d marker genes arranged in %d sets.'
% (taxon, numMarkers, numMarkerSets))
self.logger.info(
' Marker set inferred from %d reference genomes.' %
markerSet.numGenomes)
markerSet.lineageStr = taxon
binMarkerSets.addMarkerSet(markerSet)
fout = open(markerFile, 'w')
fout.write(DefaultValues.TAXON_MARKER_FILE_HEADER + '\n')
binMarkerSets.write(fout)
fout.close()
return True
def markerSet(self, rank, taxon, markerFile):
"""Obtain specified taxonomic-specific marker set."""
taxonMarkerSets = self.readMarkerSets()
if rank not in taxonMarkerSets:
self.logger.error(' Unrecognized taxonomic rank: ' + rank)
return False
elif taxon not in taxonMarkerSets[rank]:
self.logger.error(' Unrecognized taxon: %s (in rank %s): ' % (taxon, rank))
return False
markerSet = taxonMarkerSets[rank][taxon]
taxonomy = markerSet.lineageStr.split(';')[::-1]
binMarkerSets = BinMarkerSets(taxon, BinMarkerSets.TAXONOMIC_MARKER_SET)
for i, taxon in enumerate(taxonomy):
if rank != 'life':
rank = ranksByLevel[len(taxonomy)-i-1]
if rank == 'species':
taxon = taxonomy[1] + ' ' + taxonomy[0]
markerSet = taxonMarkerSets[rank][taxon]
numMarkers, numMarkerSets = markerSet.size()
self.logger.info(' Marker set for %s contains %d marker genes arranged in %d sets.' % (taxon, numMarkers, numMarkerSets))
self.logger.info(' Marker set inferred from %d reference genomes.' % markerSet.numGenomes)
markerSet.lineageStr = taxon
binMarkerSets.addMarkerSet(markerSet)
fout = open(markerFile, 'w')
fout.write(DefaultValues.TAXON_MARKER_FILE_HEADER + '\n')
binMarkerSets.write(fout)
fout.close()
return True
def getBinMarkerSets(self, outDir, markerFile, numGenomesMarkers,
bootstrap, bNoLineageSpecificRefinement, bForceDomain,
bRequireTaxonomy, resultsParser, minUnique, maxMulti):
"""Determine marker sets for each bin."""
self.logger.info(' Determining marker sets for each genome bin.')
# get all bin ids
binIds = getBinIdsFromOutDir(outDir)
# get statistics for internal nodes
uniqueIdToLineageStatistics = self.readNodeMetadata()
# determine marker set for each bin
treeFile = os.path.join(outDir, 'storage', 'tree',
DefaultValues.PPLACER_TREE_OUT)
tree = dendropy.Tree.get_from_path(treeFile,
schema='newick',
rooting="force-rooted",
preserve_underscores=True)
rootNode = tree.find_node(filter_fn=lambda n: n.parent_node == None)
fout = open(markerFile, 'w')
fout.write(DefaultValues.LINEAGE_MARKER_FILE_HEADER + '\n')
numProcessedBins = 0
statusStr = ''
for binId in binIds:
if self.logger.getEffectiveLevel() <= logging.INFO:
numProcessedBins += 1
sys.stderr.write(' ' * len(statusStr) +
'\r') # clear previous line
statusStr = ' Finished processing %d of %d (%.2f%%) bins (current: %s).' % (
numProcessedBins, len(binIds),
float(numProcessedBins) * 100 / len(binIds), binId)
sys.stderr.write('%s\r' % statusStr)
sys.stderr.flush()
node = tree.find_node_with_taxon_label(binId)
binMarkerSets = BinMarkerSets(binId, BinMarkerSets.TREE_MARKER_SET)
if node == None:
# bin is not in tree
node, markerSet = self.__getMarkerSet(
rootNode, tree, uniqueIdToLineageStatistics,
numGenomesMarkers, bootstrap, bForceDomain,
bRequireTaxonomy)
binMarkerSets.addMarkerSet(markerSet)
else:
# special case: if node is on the bacterial or archaeal branch descendant from the root,
# then move down the tree to include the domain-specific marker set
parentNode = node.parent_node
while parentNode != None:
if parentNode.label:
bRoot = (parentNode.parent_node == None)
break
parentNode = parentNode.parent_node
if bRoot:
# since the root is the first labeled node, we need to descend the
# tree to incorporate the domain-specific marker set
domainNode = self.__findDomainNode(node)
curNode = domainNode.child_nodes()[0]
else:
curNode = node
# get lineage specific refinement for first node with an id
if not bNoLineageSpecificRefinement:
uniqueId = parentNode.label.split('|')[0]
self.__readLineageSpecificGenesToRemove()
lineageSpecificRefinement = self.lineageSpecificGenesToRemove[
uniqueId]
# ascend tree to root, recording all marker sets meeting selection criteria
while curNode.parent_node != None:
uniqueHits, multiCopyHits = resultsParser.results[
binId].countUniqueHits()
tempForceDomain = bForceDomain or (
uniqueHits < minUnique) or (multiCopyHits > maxMulti)
curNode, markerSet = self.__getMarkerSet(
curNode.parent_node, tree, uniqueIdToLineageStatistics,
numGenomesMarkers, bootstrap, tempForceDomain,
bRequireTaxonomy)
if not bNoLineageSpecificRefinement:
markerSet = self.__removeInvalidLineageMarkerGenes(
markerSet, lineageSpecificRefinement)
binMarkerSets.addMarkerSet(markerSet)
binMarkerSets.write(fout)
if self.logger.getEffectiveLevel() <= logging.INFO:
sys.stderr.write('\n')
fout.close()
def getBinMarkerSets(self, outDir, markerFile,
numGenomesMarkers,
bootstrap, bNoLineageSpecificRefinement,
bForceDomain, bRequireTaxonomy,
resultsParser, minUnique, maxMulti):
"""Determine marker sets for each bin."""
self.logger.info(' Determining marker sets for each genome bin.')
# get all bin ids
binIds = getBinIdsFromOutDir(outDir)
# get statistics for internal nodes
uniqueIdToLineageStatistics = self.readNodeMetadata()
# determine marker set for each bin
treeFile = os.path.join(outDir, 'storage', 'tree', DefaultValues.PPLACER_TREE_OUT)
tree = dendropy.Tree.get_from_path(treeFile, schema='newick', as_rooted=True, preserve_underscores=True)
rootNode = tree.find_node(filter_fn = lambda n: n.parent_node == None)
fout = open(markerFile, 'w')
fout.write(DefaultValues.LINEAGE_MARKER_FILE_HEADER + '\n')
numProcessedBins = 0
for binId in binIds:
if self.logger.getEffectiveLevel() <= logging.INFO:
numProcessedBins += 1
statusStr = ' Finished processing %d of %d (%.2f%%) bins.' % (numProcessedBins, len(binIds), float(numProcessedBins)*100/len(binIds))
sys.stderr.write('%s\r' % statusStr)
sys.stderr.flush()
node = tree.find_node_with_taxon_label(binId)
binMarkerSets = BinMarkerSets(binId, BinMarkerSets.TREE_MARKER_SET)
if node == None:
# bin is not in tree
node, markerSet = self.__getMarkerSet(rootNode, tree, uniqueIdToLineageStatistics,
numGenomesMarkers, bootstrap,
bForceDomain, bRequireTaxonomy)
binMarkerSets.addMarkerSet(markerSet)
else:
# special case: if node is on the bacterial or archaeal branch descendant from the root,
# then move down the tree to include the domain-specific marker set
parentNode = node.parent_node
while parentNode != None:
if parentNode.label:
bRoot = (parentNode.parent_node == None)
break
parentNode = parentNode.parent_node
if bRoot:
# since the root is the first labeled node, we need to descend the
# tree to incorporate the domain-specific marker set
domainNode = self.__findDomainNode(node)
curNode = domainNode.child_nodes()[0]
else:
curNode = node
# get lineage specific refinement for first node with an id
if not bNoLineageSpecificRefinement:
uniqueId = parentNode.label.split('|')[0]
self.__readLineageSpecificGenesToRemove()
lineageSpecificRefinement = self.lineageSpecificGenesToRemove[uniqueId]
# ascend tree to root, recording all marker sets meeting selection criteria
while curNode.parent_node != None:
uniqueHits, multiCopyHits = resultsParser.results[binId].countUniqueHits()
tempForceDomain = bForceDomain or (uniqueHits < minUnique) or (multiCopyHits > maxMulti)
curNode, markerSet = self.__getMarkerSet(curNode.parent_node, tree, uniqueIdToLineageStatistics,
numGenomesMarkers, bootstrap,
tempForceDomain, bRequireTaxonomy)
if not bNoLineageSpecificRefinement:
markerSet = self.__removeInvalidLineageMarkerGenes(markerSet, lineageSpecificRefinement)
binMarkerSets.addMarkerSet(markerSet)
binMarkerSets.write(fout)
if self.logger.getEffectiveLevel() <= logging.INFO:
sys.stderr.write('\n')
fout.close()
