def write_json(self): jw = RefJsonBuilder() jw.set_branch_tax_map(self.bid_ranks_map) jw.set_tree(self.reftree_lbl_str) jw.set_outgroup(self.reftree_outgroup) jw.set_ratehet_model(self.cfg.raxml_model) jw.set_tax_tree(self.reftree_multif) jw.set_pattern_compression(self.cfg.compress_patterns) jw.set_taxcode(self.cfg.taxcode_name) jw.set_merged_ranks_map(self.input_validator.merged_ranks) corr_ranks_reverse = dict( (reversed(item) for item in self.input_validator.corr_ranks.items())) jw.set_corr_ranks_map(corr_ranks_reverse) corr_seqid_reverse = dict( (reversed(item) for item in self.input_validator.corr_seqid.items())) jw.set_corr_seqid_map(corr_seqid_reverse) mdata = { "ref_tree_size": self.reftree_size, "ref_alignment_width": self.refalign_width, "raxml_version": self.raxml_version, "timestamp": str(datetime.datetime.now()), "invocation_epac": self.invocation_epac, "invocation_raxml_multif": self.invocation_raxml_multif, "invocation_raxml_optmod": self.invocation_raxml_optmod, "invocation_raxml_epalbl": self.invocation_raxml_epalbl, "reftree_loglh": self.reftree_loglh } jw.set_metadata(mdata) seqs = self.reduced_refalign_seqs.get_entries() jw.set_sequences(seqs) if not self.cfg.no_hmmer: self.build_hmm_profile(jw) orig_tax = self.taxonomy_map jw.set_origin_taxonomy(orig_tax) self.cfg.log.debug("Calculating the speciation rate...\n") tp = tree_param(tree=self.reftree_lbl_str, origin_taxonomy=orig_tax) jw.set_rate(tp.get_speciation_rate_fast()) jw.set_nodes_height(self.node_height_map) jw.set_binary_model(self.optmod_fname) self.cfg.log.debug("Writing down the reference file...\n") jw.dump(self.cfg.refjson_fname)
def write_json(self): jw = RefJsonBuilder() jw.set_branch_tax_map(self.bid_ranks_map) jw.set_tree(self.reftree_lbl_str) jw.set_outgroup(self.reftree_outgroup) jw.set_ratehet_model(self.cfg.raxml_model) jw.set_tax_tree(self.reftree_multif) jw.set_pattern_compression(self.cfg.compress_patterns) jw.set_taxcode(self.cfg.taxcode_name) jw.set_merged_ranks_map(self.input_validator.merged_ranks) corr_ranks_reverse = dict((reversed(item) for item in self.input_validator.corr_ranks.items())) jw.set_corr_ranks_map(corr_ranks_reverse) corr_seqid_reverse = dict((reversed(item) for item in self.input_validator.corr_seqid.items())) jw.set_corr_seqid_map(corr_seqid_reverse) mdata = { "ref_tree_size": self.reftree_size, "ref_alignment_width": self.refalign_width, "raxml_version": self.raxml_version, "timestamp": str(datetime.datetime.now()), "invocation_epac": self.invocation_epac, "invocation_raxml_multif": self.invocation_raxml_multif, "invocation_raxml_optmod": self.invocation_raxml_optmod, "invocation_raxml_epalbl": self.invocation_raxml_epalbl, "reftree_loglh": self.reftree_loglh } jw.set_metadata(mdata) seqs = self.reduced_refalign_seqs.get_entries() jw.set_sequences(seqs) if not self.cfg.no_hmmer: self.build_hmm_profile(jw) orig_tax = self.taxonomy_map jw.set_origin_taxonomy(orig_tax) self.cfg.log.debug("Calculating the speciation rate...\n") tp = tree_param(tree = self.reftree_lbl_str, origin_taxonomy = orig_tax) jw.set_rate(tp.get_speciation_rate_fast()) jw.set_nodes_height(self.node_height_map) jw.set_binary_model(self.optmod_fname) self.cfg.log.debug("Writing down the reference file...\n") jw.dump(self.cfg.refjson_fname)
def write_json(self): jw = RefJsonBuilder() jw.set_taxonomy(self.bid_ranks_map) jw.set_tree(self.reftree_lbl_str) jw.set_outgroup(self.reftree_outgroup) jw.set_ratehet_model(self.cfg.raxml_model) jw.set_tax_tree(self.reftree_multif) jw.set_pattern_compression(self.cfg.compress_patterns) mdata = { "ref_tree_size": self.reftree_size, "ref_alignment_width": self.refalign_width, "raxml_version": self.raxml_version, "timestamp": str(datetime.datetime.now()), "invocation_epac": self.invocation_epac, "invocation_raxml_multif": self.invocation_raxml_multif, "invocation_raxml_optmod": self.invocation_raxml_optmod, "invocation_raxml_epalbl": self.invocation_raxml_epalbl } jw.set_metadata(mdata) seqs = self.reduced_refalign_seqs.get_entries() jw.set_sequences(seqs) if not self.cfg.no_hmmer: self.build_hmm_profile(jw) orig_tax = self.taxonomy_map jw.set_origin_taxonomy(orig_tax) print "Calculating the speciation rate...\n" tp = tree_param(tree = self.reftree_lbl_str, origin_taxonomy = orig_tax) jw.set_rate(tp.get_speciation_rate_fast()) jw.set_nodes_height(self.node_height_map) jw.set_binary_model(self.optmod_fname) print "Writing down the reference file...\n" jw.dump(self.cfg.refjson_fname)