示例#1
0
    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)
示例#2
0
    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)
示例#3
0
    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)