// =============================================================== // // // // File : GEN_translations.cxx // // Purpose : supports removal of redundant translations of // // gene CDS // // // // Coded by Ralf Westram (coder@reallysoft.de) in January 2009 // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include "GEN_local.hxx" #include #include #include #include using namespace std; // ------------------------------------------------- // remove redundant translations from genes // @@@ add menu-entry to genome-NTREE ("Remove reproducible translations") static char *translate_gene_sequence(GBDATA *gb_gene, GB_ERROR& error, int& translated_length, char *startCodon) { // return translation of gene sequence // the start codon is copied into result buffer 'startCodon' (has to be sized 4 bytes) size_t gene_length; char *gene_seq = GBT_read_gene_sequence_and_length(gb_gene, true, 0, &gene_length); if (!gene_seq) error = GB_await_error(); else { // store start codon in result buffer: memcpy(startCodon, gene_seq, 3); startCodon[3] = 0; int arb_transl_table, codon_start; error = translate_getInfo(gb_gene, arb_transl_table, codon_start); if (arb_transl_table == -1) arb_transl_table = TTIT_embl2arb(1); // use embl table 1 (standard code) if (codon_start == -1) codon_start = 0; // default codon start if (!error) translate_nuc2aa(arb_transl_table, gene_seq, gene_length, codon_start, false, true, true, &translated_length); if (error) { free(gene_seq); gene_seq = NULp; } } return gene_seq; } enum GEN_remove_state { GRS_NO_CHANGE = 0, // no translation found GRS_FAILED = 1, // error is set GRS_TRANSLATION_REMOVED = 2, // translation was present, reproducible and has been removed GRS_TRANSLATION_FAILED = 4, // translation differed (wrote ARB translation to field 'ARB_translation') GRS_START_CODON_WRONG = 8, // translation differed only in start codon GRS_NOTE_ADDED = 16, // note has been added }; static GEN_remove_state remove_redundant_translation(GBDATA *gb_gene, bool ignore_start_codon_error, char *errornousCodon, GB_ERROR &error) { // If translation can be re-produced by ARB, // it will be removed // ('ARB_translation' will be removed as well in this case) // Otherwise // a field 'ARB_translation' is inserted, which contains the translation generated by ARB. // // If result is GRS_START_CODON_WRONG, the questionable codon is copied into errornousCodon. // (errornousCodon has to be a buffer with size == 4) // @@@ If another code or codonstart translates fine, a hint shall be written to field 'translation_hint' GEN_remove_state result = GRS_NO_CHANGE; char *add_note = NULp; // will be added as 'ARB_translation_note' (if set) error = NULp; #define set_result_bit(s) result = GEN_remove_state(result|s) GBDATA *gb_translation = GB_entry(gb_gene, "translation"); if (gb_translation) { int translated_length; char *generated = translate_gene_sequence(gb_gene, error, translated_length, errornousCodon); if (!generated || translated_length<1) { // insert note and continue add_note = GBS_global_string_copy("Failed to translate gene-sequence (%s)", error); error = NULp; set_result_bit(GRS_TRANSLATION_FAILED); } else { if (generated[translated_length-1] == '*') { generated[--translated_length] = 0; // cut off stop codon } const char *original = GB_read_char_pntr(gb_translation); bool remove = false; if (strcmp(generated+1, original+1) == 0) { // most of translation matches if (generated[0] == original[0]) { // start codon matches remove = true; } else { // start codon differs set_result_bit(GRS_START_CODON_WRONG); // report remove = ignore_start_codon_error; // and delete if requested } } if (remove) { // remove translation and related entries const char *to_remove[] = { "translation", "ARB_translation", "ARB_translation_note", NULp }; GB_ERROR err = NULp; int failed_field = -1; for (int r = 0; to_remove[r] && !err; ++r) { GBDATA *gb_remove = GB_entry(gb_gene, to_remove[r]); if (gb_remove) { err = GB_delete(gb_remove); if (err) failed_field = r; } } if (err) error = GBS_global_string("Failed to delete field '%s' (%s)", to_remove[failed_field], err); else { error = GBT_write_byte(gb_gene, "ARB_translation_rm", 1); if (!error) set_result_bit(GRS_TRANSLATION_REMOVED); } } else { error = GBT_write_string(gb_gene, "ARB_translation", generated); if (!error) set_result_bit(GRS_TRANSLATION_FAILED); } } free(generated); } if (add_note && !error) { error = GBT_write_string(gb_gene, "ARB_translation_note", add_note); set_result_bit(GRS_NOTE_ADDED); } if (error) result = GRS_FAILED; free(add_note); return result; #undef set_result_bit } GB_ERROR GEN_testAndRemoveTranslations(GBDATA *gb_gene_data, void (*warn)(AW_CL cd, const char *msg), AW_CL cd, AW_repeated_question *ok_to_ignore_wrong_start_codon) { int ok = 0; // identical translations int failed = 0; // non-identical translations int wrong_start_codon = 0; // translations where start_codon differed int no_entry = 0; // genes w/o 'translation' entry int note_added = 0; // count gene for which a note has been added GB_ERROR error = NULp; const int possibleCodons = 4*4*4; GB_HASH *wrongStartCodons = GBS_create_hash(possibleCodons, GB_IGNORE_CASE); for (GBDATA *gb_gene = GB_entry(gb_gene_data, "gene"); gb_gene && !error; gb_gene = GB_nextEntry(gb_gene)) { int retry = 0; for (int Try = 0; Try <= retry && !error; Try++) { error = NULp; char startCodon[4]; GEN_remove_state state = remove_redundant_translation(gb_gene, Try, startCodon, error); switch (state) { case GRS_NO_CHANGE: no_entry++; break; case GRS_FAILED: gen_assert(error); break; default: if (state&GRS_TRANSLATION_REMOVED) { ok++; } else { gen_assert(state&GRS_TRANSLATION_FAILED); if (Try == 0) { if (state&GRS_START_CODON_WRONG) { wrong_start_codon++; AW_repeated_question* q = ok_to_ignore_wrong_start_codon; if (q->get_answer("only_start_codon_differs", "Translation differs only in start codon", "Ignore and remove,Keep translation", "all", false) == 0) { retry++; } else { failed++; } GBS_incr_hash(wrongStartCodons, startCodon); } else if (state&GRS_NOTE_ADDED) { failed++; note_added++; } } else { failed++; } } break; } } } if (!error && failed>0) { warn(cd, GBS_global_string("%i translations could not be reproduced by ARB", failed)); static bool first_warning = true; if (first_warning) { // show details once warn(cd, "Note: Reproducible translations were removed from database.\n" " Failed translations were left in database and an additional\n" " field 'ARB_translation' was added."); warn(cd, GBS_global_string("- %i genes had no translation entry", no_entry)); warn(cd, GBS_global_string("- %i translations were reproducible", ok)); first_warning = false; } if (wrong_start_codon>0) { char *codonInfo = GBS_hashtab_2_string(wrongStartCodons); warn(cd, GBS_global_string("- %i translations had wrong start codon (%s)", wrong_start_codon, codonInfo)); free(codonInfo); } if (note_added>0) { warn(cd, GBS_global_string("- %i ARB_translation_note entries were generated. Please examine!", note_added)); } } GBS_free_hash(wrongStartCodons); return error; }