// =============================================================== // // // // File : arb_export_newick.cxx // // Purpose : used by the SILVA pipeline to export trees for // // which the tree leafs are labeled by NDS and not // // by the species ID (name) of the sequence. // // // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include #include #include #include #include #include #include using namespace std; class CLI : virtual Noncopyable { bool helpWanted; GB_ERROR error; string database; // name of input database string tree; // name of the tree to export string newick_file; // name of the file the newick tree is exported to string leaf_aci; // aci to generate the leaf names LabelQuoting quoting_mode; // none, single or double. single and double will be forced bool add_branch_length; // true -> branch lengths added to the newick tree bool add_bootstraps; // true -> bootstrap values added to the newick tree bool add_group_names; // true -> group names added to the newick tree bool replace_problem_chars; // true -> problem chars are replaced in the newick tree bool pretty; // true -> prettify the newick tree static inline const char *getarg(int& argc, const char**& argv) { return argc>0 ? (--argc,*argv++) : NULp; } inline const char *expect_arg(int& argc, const char**& argv) { const char *arg = getarg(argc, argv); if (!arg) { error = "expected argument missing"; arg = ""; } return arg; } inline LabelQuoting parse_quoting_mode(int& argc, const char**& argv) { const char *quoting_mode_str= expect_arg(argc, argv); if (strcasecmp(quoting_mode_str, "none") == 0) { return LABEL_DISALLOW_QUOTES; } else if (strcasecmp(quoting_mode_str, "single") == 0) { return LabelQuoting(LABEL_SINGLE_QUOTES | LABEL_FORCE_QUOTES); } else if (strcasecmp(quoting_mode_str, "double") == 0) { return LabelQuoting(LABEL_DOUBLE_QUOTES | LABEL_FORCE_QUOTES); } else { error = GBS_global_string("unknown quoting mode '%s'", quoting_mode_str); return LABEL_DISALLOW_QUOTES; } } void parse(int& argc, const char**& argv) { const char *arg = getarg(argc, argv); if (arg) { if (strcmp(arg, "--db") == 0) database = expect_arg(argc, argv); else if (strcmp(arg, "--tree") == 0) tree = expect_arg(argc, argv); else if (strcmp(arg, "--newick-file") == 0) newick_file = expect_arg(argc, argv); else if (strcmp(arg, "--leaf-aci") == 0) leaf_aci = expect_arg(argc, argv); else if (strcmp(arg, "--quoting") == 0) quoting_mode = parse_quoting_mode(argc, argv); else if (strcmp(arg, "--add-branch-lengths") == 0) add_branch_length = true; else if (strcmp(arg, "--add-bootstraps") == 0) add_bootstraps = true; else if (strcmp(arg, "--add-group-names") == 0) add_group_names = true; else if (strcmp(arg, "--replace-problem-chars") == 0) replace_problem_chars = true; else if (strcmp(arg, "--pretty") == 0) pretty = true; else if (strcmp(arg, "--help") == 0) helpWanted = true; else { error = GBS_global_string("unexpected argument '%s'", arg); } } } void check_required_arguments() { if (database.empty()) error = "no input database specified"; else if (tree.empty()) error = "no tree name specified"; else if (newick_file.empty()) error = "no output file specified"; } public: CLI(int argc, const char **argv) : helpWanted(false), error(NULp), leaf_aci("readdb(\"name\")"), quoting_mode(LABEL_DISALLOW_QUOTES), add_branch_length(false), add_bootstraps(false), add_group_names(false), replace_problem_chars(false), pretty(false) { --argc; ++argv; while (!error && argc>0 && !helpWanted) { parse(argc, argv); } if (!helpWanted) { // do not check extended conditions, if '--help' seen if (!error) { check_required_arguments(); if (error) helpWanted = true; } } } void show_help() const { fputs("\n" "arb_export_newick -- export a tree in newick format\n" "Usage: arb_export_newick [switches]\n" "\n" "mandatory arguments:\n" "--db ARB database to export from\n" "--tree name of the tree to export\n" "--newick-file name of generated newick file\n" "\n" "switches:\n" "--leaf-aci specify content for the leaf names using ACI\n" " (default: \"readdb(name)\"; see http://help.arb-home.de/aci.html)\n" "--quoting none, single, double. Single and double are forced.\n" " (default: none)\n" "--add-branch-lengths add the branch lengths to the newick file.\n" " (default: branch lengths are omitted)\n" "--add-bootstraps add the bootstrap values to the newick file.\n" " (default: bootstrap values are omitted)\n" "--add-group-names add the group names to the newick file.\n" " (default: group names are omitted)\n" "--replace-problem-chars problematic characters in names will be replaced\n" " (default: no characters are replaced)\n" "--pretty prettify the newick tree\n" " (default: tree is not prettified)\n" "--help show this help message\n" "\n" ,stderr); } bool help_wanted() const { return helpWanted; } GB_ERROR get_error() const { return error; } const char *get_database() const { return database.c_str(); } const char *get_tree() const { return tree.c_str(); } const char *get_newick_file() const { return newick_file.c_str(); } const char *get_leaf_aci() const { return leaf_aci.c_str(); } LabelQuoting get_quoting_mode() const { return quoting_mode; } bool shall_add_branch_length() const { return add_branch_length; } bool shall_add_bootstraps() const { return add_bootstraps; } bool shall_add_group_names() const { return add_group_names; } bool shall_replace_problem_chars() const { return replace_problem_chars; } bool shall_be_pretty() const { return pretty; } }; class ACI_Labeler: public TreeLabeler { SmartCharPtr leaf_aci; public: explicit ACI_Labeler(const char *leaf_aci_) : leaf_aci(strdup(leaf_aci_)) {} const char *speciesLabel(GBDATA *gb_main, GBDATA *gb_species, TreeNode *, const char *tree_name) const OVERRIDE { GBL_env env(gb_main, tree_name); GBL_call_env callEnv(gb_species, env); char* node_text = GB_command_interpreter_in_env("", leaf_aci.content(), callEnv); if (!node_text) { GB_ERROR ndsError = GB_await_error(); node_text = GBS_global_string_copy("", ndsError); GB_export_error(ndsError); } RETURN_LOCAL_ALLOC(node_text); } const char *groupLabel(GBDATA *, GBDATA *, TreeNode *innerNode, const char *) const { // ACI is not used for group names return innerNode->name; } }; static GB_ERROR export_newick(const CLI& args) { ARB_redirect_handlers_to(stderr, stderr); GB_ERROR error = NULp; const char *dbname = args.get_database(); GB_shell shell; GBDATA *gb_main = GB_open(dbname, "r"); if (!gb_main) { error = GB_await_error(); } else { ACI_Labeler labeler(args.get_leaf_aci()); LabelQuoting quoting_mode = args.get_quoting_mode(); if (args.shall_replace_problem_chars()) { quoting_mode = LabelQuoting(quoting_mode|LABEL_FORCE_REPLACE); } error = TREE_write_Newick(gb_main, args.get_tree(), labeler, args.shall_add_branch_length(), args.shall_add_bootstraps(), args.shall_add_group_names(), args.shall_be_pretty(), quoting_mode, args.get_newick_file()); // get possible NDS error, too if (!error) error = GB_incur_error(); GB_close(gb_main); } return error; } int main(int argc, char **argv) { CLI args(argc, const_cast(argv)); GB_ERROR error = args.get_error(); if (!error && args.help_wanted()) { args.show_help(); return EXIT_FAILURE; } if (!error) error = export_newick(args); if (error) { fprintf(stderr, "Error: %s\n", error); return EXIT_FAILURE; } return EXIT_SUCCESS; }