GtStr* gt_get_gtdata_path(const char *prog, GtError *err) { GtStr *path; const char **defaultpath; int had_err = 0; gt_error_check(err); gt_assert(prog); path = gt_str_new(); had_err = gt_file_find_exec_in_path(path, prog, err); if (!had_err) { gt_assert(gt_str_length(path)); gt_str_append_cstr(path, GTDATADIR); if (gt_file_exists_and_is_dir(gt_str_get(path))) return path; gt_str_set_length(path, gt_str_length(path) - strlen(GTDATADIR)); gt_str_append_cstr(path, UPDIR); gt_str_append_cstr(path, GTDATADIR); if (gt_file_exists_and_is_dir(gt_str_get(path))) return path; for (defaultpath = GTDATA_DEFAULT_PATHS; *defaultpath; defaultpath++) { gt_str_reset(path); gt_str_append_cstr(path, *defaultpath); if (gt_file_exists_and_is_dir(gt_str_get(path))) return path; } if (!gt_file_exists_and_is_dir(gt_str_get(path))) { gt_error_set(err, "could not find gtdata%c directory", GT_PATH_SEPARATOR); had_err = -1; } } if (had_err) { gt_str_delete(path); return NULL; } return path; }
int gt_condenseq_output_to_gff3(const GtCondenseq *condenseq, GtError *err) { int had_err = 0; GtUword idx, name_len, seqnum = 0, seqstart = 0, seqend = 0, desclen; GtStr *filename = NULL, *id = gt_str_new_cstr("U"), *name = gt_str_new_cstr("unique"), *parent_unique = gt_str_new_cstr("U"), *seqid = gt_str_new(), *source = gt_str_new_cstr("Condenseq"); GtFile *outfile = NULL; GtGFF3Visitor *gffv = NULL; GtNodeVisitor *nodev = NULL; GtFeatureNode *fnode = NULL; GtGenomeNode *node = NULL; GtRange range; gt_assert(condenseq != NULL); filename = gt_str_new_cstr(gt_condenseq_basefilename(condenseq)); name_len = gt_str_length(name); gt_str_append_cstr(filename, ".gff3"); outfile = gt_file_new(gt_str_get(filename), "w", err); nodev = gt_gff3_visitor_new(outfile); gffv = (GtGFF3Visitor *) nodev; gt_gff3_visitor_retain_id_attributes(gffv); node = gt_feature_node_new(seqid, "experimental_feature", (GtUword) 1, (GtUword) 1, GT_STRAND_BOTH); fnode = (GtFeatureNode*) node; gt_feature_node_set_source(fnode, source); for (idx = 0; !had_err && idx < condenseq->udb_nelems; ++idx) { GtCondenseqUnique uq = condenseq->uniques[idx]; if (seqend <= uq.orig_startpos) { const char *desc; gt_genome_node_delete(node); seqnum = gt_condenseq_pos2seqnum(condenseq, uq.orig_startpos); seqstart = gt_condenseq_seqstartpos(condenseq, seqnum); seqend = seqstart + condenseq_seqlength_help(condenseq, seqnum, seqstart); desc = gt_condenseq_description(condenseq, &desclen, seqnum); gt_str_reset(seqid); gt_str_append_cstr_nt(seqid, desc, desclen); node = gt_feature_node_new(seqid, "experimental_feature", (GtUword) 1, (GtUword) 1, GT_STRAND_BOTH); fnode = (GtFeatureNode*) node; gt_feature_node_set_source(fnode, source); } gt_str_set_length(name, name_len); gt_str_append_uword(name, idx); gt_str_set_length(id, (GtUword) 1); gt_str_append_uword(id, idx); gt_feature_node_set_attribute(fnode, "Name", gt_str_get(name)); gt_feature_node_set_attribute(fnode, "ID", gt_str_get(id)); /* 1 Based coordinates! */ range.start = uq.orig_startpos + 1 - seqstart; range.end = uq.orig_startpos + uq.len - seqstart; gt_genome_node_set_range(node, &range); had_err = gt_genome_node_accept(node, nodev, err); } gt_str_reset(name); gt_str_append_cstr(name, "link"); gt_str_reset(id); gt_str_append_cstr(id, "L"); name_len = gt_str_length(name); seqend = 0; for (idx = 0; !had_err && idx < condenseq->ldb_nelems; ++idx) { GtCondenseqLink link = condenseq->links[idx]; if (seqend <= link.orig_startpos) { const char *desc; gt_genome_node_delete(node); seqnum = gt_condenseq_pos2seqnum(condenseq, link.orig_startpos); seqstart = gt_condenseq_seqstartpos(condenseq, seqnum); seqend = seqstart + condenseq_seqlength_help(condenseq, seqnum, seqstart); desc = gt_condenseq_description(condenseq, &desclen, seqnum); gt_str_reset(seqid); gt_str_append_cstr_nt(seqid, desc, desclen); node = gt_feature_node_new(seqid, "experimental_feature", (GtUword) 1, (GtUword) 1, GT_STRAND_BOTH); fnode = (GtFeatureNode*) node; gt_feature_node_set_source(fnode, source); } gt_str_set_length(name, name_len); gt_str_append_uword(name, idx); gt_str_set_length(id, (GtUword) 1); gt_str_append_uword(id, idx); gt_feature_node_set_attribute(fnode, "Name", gt_str_get(name)); gt_feature_node_set_attribute(fnode, "ID", gt_str_get(id)); gt_str_set_length(parent_unique, (GtUword) 1); gt_str_append_uword(parent_unique, link.unique_id); gt_feature_node_set_attribute(fnode, "Derives_from", gt_str_get(parent_unique)); /* 1 Based coordinates! */ range.start = link.orig_startpos + 1 - seqstart; range.end = link.orig_startpos + link.len - seqstart; gt_genome_node_set_range(node, &range); had_err = gt_genome_node_accept(node, nodev, err); } gt_file_delete(outfile); gt_genome_node_delete(node); gt_node_visitor_delete(nodev); gt_str_delete(filename); gt_str_delete(id); gt_str_delete(name); gt_str_delete(parent_unique); gt_str_delete(seqid); gt_str_delete(source); return had_err; }
static void remove_terminal_comma(GtStr *str) { gt_assert(str && gt_str_length(str)); if (gt_str_get(str)[gt_str_length(str)-1] == ',') gt_str_set_length(str, gt_str_length(str)-1); }
static int hmmsearch_process_coarse_hits( char *table_filename, GtCondenseq *ces, GtCondenseqHmmsearchArguments *arguments, GtLogger *logger, GtError *err) { int had_err = 0; GtStr *line = gt_str_new(); FILE *table = NULL; GtSplitter *splitter = gt_splitter_new(); GtStr *query = gt_str_new(), *fine_fasta_filename = gt_str_new_cstr("condenseq"); GtRBTree *sequences = NULL; GtUword filecount = (GtUword) 1; unsigned int querycount = 0; const GtUword fine_fasta_name_length = gt_str_length(fine_fasta_filename); const GtUword table_name_length = gt_str_length(arguments->outtable_filename); table = gt_xfopen(table_filename, "r"); sequences = gt_rbtree_new(hmmsearch_cmp_seqnum, hmmsearch_tree_free_node, NULL); while (!had_err && gt_str_read_next_line(line, table) == 0) { char *c_line = gt_str_get(line); GtUword uid; const GtUword target_column = 0, query_column = (GtUword) 3; if (c_line[0] != '#') { gt_splitter_split_non_empty(splitter, c_line, gt_str_length(line), ' '); gt_assert(gt_splitter_size(splitter) == (GtUword) 23); if (sscanf(gt_splitter_get_token(splitter, target_column), GT_WU, &uid) != 1) { gt_error_set(err, "couldn't parse target number: %s", gt_splitter_get_token(splitter, target_column)); had_err = -1; } if (gt_str_length(query) == 0 || strcmp(gt_str_get(query), gt_splitter_get_token(splitter, query_column)) != 0) { gt_str_set(query, gt_splitter_get_token(splitter, query_column)); gt_logger_log(logger, "new query: %s", gt_str_get(query)); querycount++; } if (!had_err && querycount == arguments->max_queries) { hmmsearch_create_fine_fas(fine_fasta_filename, sequences, ces); if (table_name_length != 0) gt_str_append_uword(arguments->outtable_filename, filecount++); had_err = hmmsearch_call_fine_search(table_name_length != 0 ? arguments->outtable_filename : NULL, gt_str_get(fine_fasta_filename), gt_str_get(arguments->hmmsearch_path), gt_str_get(arguments->hmm), logger, err); gt_rbtree_clear(sequences); gt_str_set_length(fine_fasta_filename, fine_fasta_name_length); if (table_name_length != 0) gt_str_set_length(arguments->outtable_filename, table_name_length); querycount = 0; } if (!had_err) { if (gt_condenseq_each_redundant_seq(ces, uid, hmmsearch_process_seq, sequences, err) == 0) { had_err = -1; } } gt_splitter_reset(splitter); } gt_str_reset(line); } gt_splitter_delete(splitter); gt_str_delete(line); gt_str_delete(query); gt_xfclose(table); if (!had_err) { hmmsearch_create_fine_fas(fine_fasta_filename, sequences, ces); if (table_name_length != 0) gt_str_append_uword(arguments->outtable_filename, filecount++); had_err = hmmsearch_call_fine_search(table_name_length != 0 ? arguments->outtable_filename : NULL, gt_str_get(fine_fasta_filename), gt_str_get(arguments->hmmsearch_path), gt_str_get(arguments->hmm), logger, err); } gt_log_log("created " GT_WU " files", filecount); gt_rbtree_delete(sequences); gt_str_delete(fine_fasta_filename); return had_err; }