def load_refjson(self, refjson_fname): try: self.refjson = RefJsonParser(refjson_fname) except ValueError: self.cfg.exit_user_error("ERROR: Invalid json file format!") #validate input json format (valid, err) = self.refjson.validate() if not valid: self.cfg.log.error( "ERROR: Parsing reference JSON file failed:\n%s", err) self.cfg.exit_user_error() self.rate = self.refjson.get_rate() self.node_height = self.refjson.get_node_height() self.origin_taxonomy = self.refjson.get_origin_taxonomy() self.tax_tree = self.refjson.get_tax_tree() self.cfg.compress_patterns = self.refjson.get_pattern_compression() self.bid_taxonomy_map = self.refjson.get_branch_tax_map() if not self.bid_taxonomy_map: # old file format (before 1.6), need to rebuild this map from scratch th = TaxTreeHelper(self.cfg, self.origin_taxonomy) th.set_mf_rooted_tree(self.tax_tree) th.set_bf_unrooted_tree(self.refjson.get_reftree()) self.bid_taxonomy_map = th.get_bid_taxonomy_map() self.write_bid_tax_map(self.bid_taxonomy_map, final=False) reftree_str = self.refjson.get_raxml_readable_tree() self.reftree = Tree(reftree_str) self.reftree_size = len(self.reftree.get_leaves()) # IMPORTANT: set EPA heuristic rate based on tree size! self.cfg.resolve_auto_settings(self.reftree_size) # If we're loading the pre-optimized model, we MUST set the same rate het. mode as in the ref file if self.cfg.epa_load_optmod: self.cfg.raxml_model = self.refjson.get_ratehet_model() self.classify_helper = TaxClassifyHelper(self.cfg, self.bid_taxonomy_map, self.rate, self.node_height) self.taxtree_helper = TaxTreeHelper(self.cfg, self.origin_taxonomy, self.tax_tree) tax_code_name = self.refjson.get_taxcode() self.tax_code = TaxCode(tax_code_name) self.taxonomy = Taxonomy(prefix=EpacConfig.REF_SEQ_PREFIX, tax_map=self.origin_taxonomy) self.tax_common_ranks = self.taxonomy.get_common_ranks() # print "Common ranks: ", self.tax_common_ranks self.mislabels_cnt = [0] * TaxCode.UNI_TAX_LEVELS self.rank_mislabels_cnt = [0] * TaxCode.UNI_TAX_LEVELS
def setUp(self): self.testfile_dir = os.path.join( os.path.dirname(os.path.abspath(__file__)), "testfiles") self.tax_fname = os.path.join(self.testfile_dir, "test_clean.tax") cfg = EpacClassifierConfig() map_fname = os.path.join(self.testfile_dir, "bid_tax_map2.txt") self.bid_tax_map = {} with open(map_fname) as inf: for line in inf: bid, rank_id, rdiff, brlen = line.strip().split("\t") self.bid_tax_map[bid] = (rank_id, int(rdiff), float(brlen)) self.classify_helper = TaxClassifyHelper(cfg, self.bid_tax_map)
def __init__(self, config, args): self.cfg = config self.jplace_fname = args.jplace_fname self.ignore_refalign = args.ignore_refalign self.tmp_refaln = config.tmp_fname("%NAME%.refaln") #here is the final alignment file for running EPA self.epa_alignment = config.tmp_fname("%NAME%.afa") self.hmmprofile = config.tmp_fname("%NAME%.hmmprofile") self.tmpquery = config.tmp_fname("%NAME%.tmpquery") self.noalign = config.tmp_fname("%NAME%.noalign") self.seqs = None assign_fname = args.output_name + ".assignment.txt" self.out_assign_fname = os.path.join(args.output_dir, assign_fname) jplace_fname = args.output_name + ".jplace" self.out_jplace_fname = os.path.join(args.output_dir, jplace_fname) try: self.refjson = RefJsonParser(config.refjson_fname) except ValueError: self.cfg.exit_user_error("Invalid json file format: %s" % config.refjson_fname) #validate input json format self.refjson.validate() self.reftree = self.refjson.get_reftree() self.rate = self.refjson.get_rate() self.node_height = self.refjson.get_node_height() self.cfg.compress_patterns = self.refjson.get_pattern_compression() self.bid_taxonomy_map = self.refjson.get_branch_tax_map() if not self.bid_taxonomy_map: # old file format (before 1.6), need to rebuild this map from scratch th = TaxTreeHelper(self.cfg, self.refjson.get_origin_taxonomy()) th.set_mf_rooted_tree(self.refjson.get_tax_tree()) th.set_bf_unrooted_tree(self.refjson.get_reftree()) self.bid_taxonomy_map = th.get_bid_taxonomy_map() self.cfg.log.info("Loaded reference tree with %d taxa\n" % len(self.reftree.get_leaves())) self.classify_helper = TaxClassifyHelper(self.cfg, self.bid_taxonomy_map, self.rate, self.node_height)
def run_final_epa_test(self): self.reftree_outgroup = self.refjson.get_outgroup() pruned_reftree = self.prune_mislabels_from_tree( self.reftree, "reference") pruned_taxtree = self.prune_mislabels_from_tree( self.reftree, "taxonomic") # remove unifurcation at the root if len(pruned_reftree.children) == 1: pruned_reftree = pruned_reftree.children[0] self.mislabels = [] th = TaxTreeHelper(self.cfg, self.origin_taxonomy) th.set_mf_rooted_tree(pruned_taxtree) reftree_epalbl_str = None if self.cfg.final_jplace_fname: if os.path.isdir(self.cfg.final_jplace_fname): jplace_fmask = os.path.join(self.cfg.final_jplace_fname, '*.jplace') else: jplace_fmask = self.cfg.final_jplace_fname jplace_fname_list = glob.glob(jplace_fmask) placements = [] for jplace_fname in jplace_fname_list: jp = EpaJsonParser(jplace_fname) placements += jp.get_placement() if not reftree_epalbl_str: reftree_epalbl_str = jp.get_std_newick_tree() config.log.debug("Loaded %d final epa placements from %s\n", len(placements), jplace_fmask) else: epa_result = self.run_epa_once(pruned_reftree) reftree_epalbl_str = epa_result.get_std_newick_tree() placements = epa_result.get_placement() # update branchid-taxonomy mapping to account for possible changes in branch numbering reftree_tax = Tree(reftree_epalbl_str) th.set_bf_unrooted_tree(reftree_tax) bid_tax_map = th.get_bid_taxonomy_map() self.write_bid_tax_map(bid_tax_map, final=True) cl = TaxClassifyHelper(self.cfg, bid_tax_map, self.rate, self.node_height) # newtax_fname = self.cfg.subst_name("newtax_%NAME%.tre") # th.get_tax_tree().write(outfile=newtax_fname, format=3) final_ass = {} for place in placements: seq_name = place["n"][0] # get original taxonomic label orig_ranks = self.taxtree_helper.get_seq_ranks_from_tree(seq_name) # EXPERIMENTAL FEATURE - disabled for now! # It could happen that certain ranks were present in the "original" reference tree, but # are completely missing in the pruned tree (e.g., all seqs of a species were considered "suspicious" # after the leave-one-out test and thus pruned) # In this case, EPA has no chance to infer full original taxonomic annotation (=species) since the corresponding clade # is now missing. To account for this fact, we amend the original taxonomic annotation and set ranks missing from # pruned tree to "Undefined". # orig_ranks = th.strip_missing_ranks(orig_ranks) # print orig_ranks # get EPA tax label ranks, lws = cl.classify_seq(place["p"]) final_ass[seq_name] = (ranks, lws) #print seq_name, ": ", orig_ranks, "--->", ranks # check if they match mis_rec = self.check_seq_tax_labels(seq_name, orig_ranks, ranks, lws) self.write_assignments(final_ass, final=True)
def run_final_epa_test(self): self.reftree_outgroup = self.refjson.get_outgroup() tmp_reftree = self.reftree.copy(method="newick") name2refnode = {} for leaf in tmp_reftree.iter_leaves(): name2refnode[leaf.name] = leaf tmp_taxtree = self.tax_tree.copy(method="newick") name2taxnode = {} for leaf in tmp_taxtree.iter_leaves(): name2taxnode[leaf.name] = leaf for mis_rec in self.mislabels: rname = mis_rec['name'] # rname = EpacConfig.REF_SEQ_PREFIX + name if rname in name2refnode: name2refnode[rname].delete() else: print "Node not found in the reference tree: %s" % rname if rname in name2taxnode: name2taxnode[rname].delete() else: print "Node not found in the taxonomic tree: %s" % rname # remove unifurcation at the root if len(tmp_reftree.children) == 1: tmp_reftree = tmp_reftree.children[0] self.mislabels = [] th = TaxTreeHelper(self.cfg, self.origin_taxonomy) th.set_mf_rooted_tree(tmp_taxtree) epa_result = self.run_epa_once(tmp_reftree) reftree_epalbl_str = epa_result.get_std_newick_tree() placements = epa_result.get_placement() # update branchid-taxonomy mapping to account for possible changes in branch numbering reftree_tax = Tree(reftree_epalbl_str) th.set_bf_unrooted_tree(reftree_tax) bid_tax_map = th.get_bid_taxonomy_map() self.write_bid_tax_map(bid_tax_map, final=True) cl = TaxClassifyHelper(self.cfg, bid_tax_map, self.rate, self.node_height) # newtax_fname = self.cfg.subst_name("newtax_%NAME%.tre") # th.get_tax_tree().write(outfile=newtax_fname, format=3) final_ass = {} for place in placements: seq_name = place["n"][0] # get original taxonomic label orig_ranks = self.taxtree_helper.get_seq_ranks_from_tree(seq_name) # EXPERIMENTAL FEATURE - disabled for now! # It could happen that certain ranks were present in the "original" reference tree, but # are completely missing in the pruned tree (e.g., all seqs of a species were considered "suspicious" # after the leave-one-out test and thus pruned) # In this case, EPA has no chance to infer full original taxonomic annotation (=species) since the corresponding clade # is now missing. To account for this fact, we amend the original taxonomic annotation and set ranks missing from # pruned tree to "Undefined". # orig_ranks = th.strip_missing_ranks(orig_ranks) # print orig_ranks # get EPA tax label ranks, lws = cl.classify_seq(place["p"]) final_ass[seq_name] = (ranks, lws) #print seq_name, ": ", orig_ranks, "--->", ranks # check if they match mis_rec = self.check_seq_tax_labels(seq_name, orig_ranks, ranks, lws) self.write_assignments(final_ass, final=True)