// ==================================================================== // // // // File : SQ_main.cxx // // Purpose : Entrypoint to Seq. Quality analysis; calls functions // // // // // // Coded by Juergen Huber in July 2003 - February 2004 // // Coded by Kai Bader (baderk@in.tum.de) in 2007 - 2008 // // Copyright Department of Microbiology (Technical University Munich) // // // // Visit our web site at: http://www.arb-home.de/ // // // // ==================================================================== // #include "seq_quality.h" #include "SQ_functions.h" #include #include #include #include #include #include #include #include #include // -------------------------------------------------------------------------------- #define AWAR_SQ_PERM "seq_quality/" // saved in properties #define AWAR_SQ_TEMP "tmp/seq_quality/" // not saved in properties #define AWAR_SQ_WEIGHT_BASES AWAR_SQ_PERM "weight_bases" #define AWAR_SQ_WEIGHT_DEVIATION AWAR_SQ_PERM "weight_deviation" #define AWAR_SQ_WEIGHT_HELIX AWAR_SQ_PERM "weight_helix" #define AWAR_SQ_WEIGHT_CONSENSUS AWAR_SQ_PERM "weight_consensus" #define AWAR_SQ_WEIGHT_IUPAC AWAR_SQ_PERM "weight_iupac" #define AWAR_SQ_WEIGHT_GC AWAR_SQ_PERM "weight_gc" #define AWAR_SQ_MARK_ONLY_FLAG AWAR_SQ_PERM "mark_only_flag" #define AWAR_SQ_MARK_FLAG AWAR_SQ_PERM "mark_flag" #define AWAR_SQ_MARK_BELOW AWAR_SQ_PERM "mark_below" #define AWAR_SQ_REEVALUATE AWAR_SQ_PERM "reevaluate" #define AWAR_SQ_FILTER_NAME AWAR_SQ_TEMP "filter/name" void SQ_create_awars(AW_root *aw_root, AW_default aw_def) { aw_root->awar_int(AWAR_SQ_WEIGHT_BASES, 5, aw_def); aw_root->awar_int(AWAR_SQ_WEIGHT_DEVIATION, 15, aw_def); aw_root->awar_int(AWAR_SQ_WEIGHT_HELIX, 15, aw_def); aw_root->awar_int(AWAR_SQ_WEIGHT_CONSENSUS, 50, aw_def); aw_root->awar_int(AWAR_SQ_WEIGHT_IUPAC, 5, aw_def); aw_root->awar_int(AWAR_SQ_WEIGHT_GC, 10, aw_def); aw_root->awar_int(AWAR_SQ_MARK_ONLY_FLAG, 0, aw_def); aw_root->awar_int(AWAR_SQ_MARK_FLAG, 1, aw_def); aw_root->awar_int(AWAR_SQ_MARK_BELOW, 40, aw_def); aw_root->awar_int(AWAR_SQ_REEVALUATE, 0, aw_def); awt_create_filter_awars(aw_root, aw_def, AWAR_SQ_FILTER_NAME, AWAR_DEFAULT_ALIGNMENT); } // -------------------------------------------------------------------------------- inline size_t count_nodes(TreeNode *node) { // calculate number of nodes in tree return GBT_count_leafs(node)*2-1; } static void sq_calc_seq_quality_cb(AW_window *aww, adfiltercbstruct *acbs, GBDATA *gb_main) { AW_root *aw_root = aww->get_root(); GB_ERROR error = NULp; TreeNode *tree = NULp; bool marked_only = (aw_root->awar(AWAR_SQ_MARK_ONLY_FLAG)->read_int() > 0); arb_progress main_progress("Calculating sequence quality"); GB_transaction ta(gb_main); if (!error) { char *ali = GBT_get_default_alignment(gb_main); if (ali) { GB_alignment_type type = GBT_get_alignment_type(gb_main, ali); if (type == GB_AT_UNKNOWN) { error = GB_await_error(); } else if (type != GB_AT_RNA && type != GB_AT_DNA) { error = "does only support RNA/DNA sequence data"; } if (error) { error = GBS_global_string("Invalid alignment '%s' selected (%s)", ali, error); } } else { error = "No default alignment selected"; } free(ali); } if (!error) { char *treename = aw_root->awar(AWAR_TREE)->read_string(); if (treename && strcmp(treename, NO_TREE_SELECTED) != 0) { if (!error) { tree = GBT_read_tree(gb_main, treename, new SimpleRoot); if (!tree) error = GB_await_error(); else { error = GBT_link_tree(tree, gb_main, false, NULp, NULp); if (!error) { GBT_TreeRemoveType mode = marked_only ? GBT_KEEP_MARKED : GBT_REMOVE_ZOMBIES; tree = GBT_remove_leafs(tree, mode, NULp, NULp, NULp); if (!tree || tree->is_leaf()) { error = GBS_global_string("Tree contains less than 2 species after removing zombies%s", marked_only ? " and non-marked" : ""); } } } } } free(treename); } // if tree == 0 -> do basic quality calculations that are possible without tree information // otherwise -> use all groups found in tree and compare sequences against the groups they are contained in if (!error) { struct SQ_weights weights; weights.bases = aw_root->awar(AWAR_SQ_WEIGHT_BASES)->read_int(); weights.diff_from_average = aw_root->awar(AWAR_SQ_WEIGHT_DEVIATION)->read_int(); weights.helix = aw_root->awar(AWAR_SQ_WEIGHT_HELIX)->read_int(); weights.consensus = aw_root->awar(AWAR_SQ_WEIGHT_CONSENSUS)->read_int(); weights.iupac = aw_root->awar(AWAR_SQ_WEIGHT_IUPAC)->read_int(); weights.gc = aw_root->awar(AWAR_SQ_WEIGHT_GC)->read_int(); int mark_flag = aw_root->awar(AWAR_SQ_MARK_FLAG)->read_int(); int mark_below = aw_root->awar(AWAR_SQ_MARK_BELOW)->read_int(); int reevaluate = aw_root->awar(AWAR_SQ_REEVALUATE)->read_int(); // Load and use Sequence-Filter AP_filter *filter = awt_get_filter(acbs); error = awt_invalid_filter(filter); /* SQ_evaluate() generates the final estimation for the quality of an alignment. It takes the values from the different containers, which are generated by the other functions, weights them and calculates a final value. The final value is stored in "value_of_evaluation" (see options). With the values stored in "weights" one can customize how important a value stored in a container becomes for the final result. */ if (!error) { if (!tree) { if (reevaluate) { error = SQ_mark_species(gb_main, mark_below, marked_only); } else { arb_progress progress(GBT_get_species_count(gb_main)*2); SQ_GroupData *globalData = new SQ_GroupData_RNA; progress.subtitle("pass1"); error = SQ_pass1_no_tree(globalData, gb_main, filter, progress); if (!error) { progress.subtitle("pass2"); error = SQ_pass2_no_tree(globalData, gb_main, filter, progress); if (!error) { error = SQ_evaluate(gb_main, weights, marked_only); if (mark_flag && !error) { error = SQ_mark_species(gb_main, mark_below, marked_only); } } } if (error) progress.done(); delete globalData; } } else { SQ_TREE_ERROR check = SQ_check_tree_structure(tree); if (check != NONE) { switch (check) { case ZOMBIE: error = "Found one or more zombies in the tree.\n" "Please remove them or use another tree before running the quality check tool."; break; case MISSING_NODE: error = "Missing node(s) or unusable tree structure.\n" "Please fix the tree before running the quality check tool."; break; default: error = "An error occurred while traversing the tree.\n" "Please fix the tree before running the quality check tool."; break; } } else if (reevaluate) { error = SQ_mark_species(gb_main, mark_below, marked_only); } else { arb_progress progress(count_nodes(tree)*2); SQ_GroupData *globalData = new SQ_GroupData_RNA; progress.subtitle("pass1"); error = SQ_pass1_on_tree(tree, gb_main, globalData, filter, progress); if (!error) { progress.subtitle("pass2"); error = SQ_pass2_on_tree(tree, gb_main, globalData, filter, progress); if (!error) { error = SQ_evaluate(gb_main, weights, marked_only); if (mark_flag && !error) { error = SQ_mark_species(gb_main, mark_below, marked_only); } } } if (error) progress.done(); delete globalData; } } } awt_destroy_filter(filter); } error = ta.close(error); if (error) aw_message(error); SQ_clear_group_dictionary(); UNCOVERED(); destroy(tree); } static void sq_remove_quality_entries_cb(AW_window*, GBDATA *gb_main) { GB_ERROR error = SQ_remove_quality_entries(gb_main); aw_message_if(error); } static AWT_config_mapping_def seq_quality_config_mapping[] = { { AWAR_SQ_WEIGHT_BASES, "wbases" }, { AWAR_SQ_WEIGHT_DEVIATION, "wdeviation" }, { AWAR_SQ_WEIGHT_HELIX, "whelix" }, { AWAR_SQ_WEIGHT_CONSENSUS, "wconsens" }, { AWAR_SQ_WEIGHT_IUPAC, "wiupac" }, { AWAR_SQ_WEIGHT_GC, "wgc" }, { AWAR_SQ_MARK_ONLY_FLAG, "onlymarked" }, { AWAR_SQ_MARK_FLAG, "markbad" }, { AWAR_SQ_MARK_BELOW, "markbelow" }, { AWAR_SQ_REEVALUATE, "reeval" }, { NULp, NULp } }; AW_window *SQ_create_seq_quality_window(AW_root *aw_root, GBDATA *gb_main) { // create window for sequence quality calculation (called only once) AW_window_simple *aws = new AW_window_simple; aws->init(aw_root, "CALC_SEQ_QUALITY", "CALCULATE SEQUENCE QUALITY"); aws->load_xfig("seq_quality.fig"); aws->at("close"); aws->callback(AW_POPDOWN); aws->create_button("CLOSE", "CLOSE", "C"); aws->at("help"); aws->callback(makeHelpCallback("seq_quality.hlp")); aws->create_button("HELP", "HELP", "H"); aws->at("base"); aws->create_input_field(AWAR_SQ_WEIGHT_BASES, 3); aws->at("deviation"); aws->create_input_field(AWAR_SQ_WEIGHT_DEVIATION, 3); aws->at("no_helices"); aws->create_input_field(AWAR_SQ_WEIGHT_HELIX, 3); aws->at("consensus"); aws->create_input_field(AWAR_SQ_WEIGHT_CONSENSUS, 3); aws->at("iupac"); aws->create_input_field(AWAR_SQ_WEIGHT_IUPAC, 3); aws->at("gc_proportion"); aws->create_input_field(AWAR_SQ_WEIGHT_GC, 3); aws->at("monly"); aws->create_toggle(AWAR_SQ_MARK_ONLY_FLAG); aws->at("mark"); aws->create_toggle(AWAR_SQ_MARK_FLAG); aws->at("mark_below"); aws->create_input_field(AWAR_SQ_MARK_BELOW, 3); aws->at("tree"); awt_create_TREE_selection_list(gb_main, aws, AWAR_TREE); aws->at("filter"); adfiltercbstruct *adfilter = awt_create_select_filter(aws->get_root(), gb_main, AWAR_SQ_FILTER_NAME); aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, adfilter)); aws->create_button("SELECT_FILTER", AWAR_SQ_FILTER_NAME); aws->at("go"); aws->callback(makeWindowCallback(sq_calc_seq_quality_cb, adfilter, gb_main)); aws->highlight(); aws->create_button("GO", "GO", "G"); aws->at("config"); AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "seq_quality", seq_quality_config_mapping); aws->at("reevaluate"); aws->label("Re-Evaluate only"); aws->create_toggle(AWAR_SQ_REEVALUATE); aws->at("remove"); aws->callback(makeWindowCallback(sq_remove_quality_entries_cb, gb_main)); aws->create_button("Remove", "Remove", "R"); return aws; }