INNER CODE UNIT · Python

info_filetype

nickjcroucher/gubbins · python/gubbins/common.py:479

                info_filetype = input_args.model_fitter, # model fitter - format of file containing evolutionary model parameters
                output_prefix = temp_working_dir + "/" + ancestral_sequence_basename, # output prefix
                outgroup_name = input_args.outgroup, # outgroup for rooting and reconstruction
                threads = input_args.threads, # number of cores to use
                verbose = input_args.verbose,
                max_pos = max_pos)
            gaps_alignment_filename = temp_working_dir + "/" + ancestral_sequence_basename + ".joint.aln"
            raw_internal_rooted_tree_filename = temp_working_dir + "/" + ancestral_sequence_basename + ".joint.tre"
            printer.print(["\nTransferring pyjar results onto original recombination-corrected tree"])
            transfer_internal_node_labels_to_tree(raw_internal_rooted_tree_filename,
                                                  temp_rooted_tree,
                                                  current_tree_name_with_internal_nodes,
                                                  "pyjar")
            os.chdir(current_directory)
            printer.print(["\nDone transfer"])
            
        else:

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