Пример #1
0
SEXP rph_tree_scale(SEXP treeStr, SEXP scaleP, SEXP nodeStr,
		    SEXP includeLeadingP) {
  TreeNode *tr = rph_tree_new(treeStr);
  double scale = NUMERIC_VALUE(scaleP);
  char *newTreeStr;
  SEXP result;

  if (nodeStr != R_NilValue) {
    TreeNode *n;
    int includeLeading=LOGICAL_VALUE(includeLeadingP);
    n = tr_get_node(tr, CHARACTER_VALUE(nodeStr));
    if (n == NULL) {
      tr_name_ancestors(tr);
      n = tr_get_node(tr, CHARACTER_VALUE(nodeStr));
      if (n == NULL)
	die("No node named %s in %s\n", CHARACTER_VALUE(nodeStr),
	    CHARACTER_VALUE(treeStr));
    }
    tr_scale_subtree(tr, n, scale, includeLeading);
  }
  else tr_scale(tr, scale);
  newTreeStr = tr_to_string(tr, 1);
  PROTECT(result = NEW_CHARACTER(1));
  SET_STRING_ELT(result, 0, mkChar(newTreeStr));
  UNPROTECT(1);
  return result;
}
Пример #2
0
int main(int argc, char *argv[]) {
  /* variables for options, with defaults */
  TreeNode *tree = NULL, *merge_tree = NULL, *extrapolate_tree = NULL;
  Hashtable *rename_hash = NULL;
  double scale_factor = 1;
  List *prune_names = NULL, *label = NULL, *labelType = NULL;
  int prune_all_but = FALSE, tree_only = FALSE, dissect = FALSE,
    name_ancestors = FALSE, with_branch = FALSE, print_branchlen=FALSE,
    inNewick=FALSE, no_branchlen = FALSE, print_distance_to_root = FALSE;
  TreeModel *mod = NULL, *merge_mod = NULL;
  char *reroot_name = NULL, *subtree_name =NULL, *get_subtree_name = NULL,
    *node_distance_name = NULL;
  
  /* other variables */
  String *suffix,  *optstr;
  char c;
  int i, opt_idx;
  TreeNode *n;

  struct option long_opts[] = {
    {"scale", 1, 0, 's'},
    {"extrapolate", 1, 0, 'e'},
    {"prune", 1, 0, 'p'},
    {"prune-all-but", 1, 0, 'P'},
    {"get-subtree", 1, 0, 'g'},
    {"merge", 1, 0, 'm'},
    {"rename", 1, 0, 'r'},
    {"tree-only", 0, 0, 't'},
    {"no-branchlen", 0, 0, 'N'},
    {"dissect", 0, 0, 'd'},
    {"name-ancestors", 0, 0, 'a'},
    {"reroot", 1, 0, 'R'},
    {"with-branch", 1, 0, 'B'},
    {"subtree", 1, 0, 'S'},
    {"branchlen", 0, 0, 'b'},
    {"newick", 0, 0, 'n'},
    {"label-subtree", 1, 0, 'L'},
    {"label-branches", 1, 0, 'l'},
    {"help", 0, 0, 'h'},
    {0, 0, 0, 0}
  };

  while ((c = getopt_long(argc, argv, "s:p:P:g:m:r:R:B:S:D:l:L:adtNbnh", 
                          long_opts, &opt_idx)) != -1) {
    switch (c) {
    case 's':
      scale_factor = get_arg_dbl_bounds(optarg, 0, INFTY);
      break;
    case 'e':
      if (!strcmp(optarg, "default")) {
        optarg = smalloc(1000 * sizeof(char));
        #if defined(__MINGW32__)
          sprintf(optarg, "%s\\data\\exoniphy\\mammals\\cftr25_hybrid.nh",
		  PHAST_HOME);
        #else
          sprintf(optarg, "%s/data/exoniphy/mammals/cftr25_hybrid.nh", 
                  PHAST_HOME);
        #endif
      }
      extrapolate_tree = tr_new_from_file(phast_fopen(optarg, "r"));
      break;
    case 'p':
      prune_names = get_arg_list(optarg);
      break;
    case 'P':
      prune_names = get_arg_list(optarg);
      prune_all_but = TRUE;
      break;
    case 'g':
      get_subtree_name = optarg;
      break;
    case 'm':
      suffix = str_new_charstr(optarg);
      str_suffix(suffix, '.');
      if (str_equals_charstr(suffix, "nh"))
        merge_tree = tr_new_from_file(phast_fopen(optarg, "r"));
      else {
        merge_mod = tm_new_from_file(phast_fopen(optarg, "r"), 1);
        merge_tree = merge_mod->tree;
      }
      break;
    case 'r':
      rename_hash = make_name_hash(optarg);
      break;
    case 't':
      tree_only = TRUE;
      break;
    case 'N':
      no_branchlen = TRUE;
      tree_only = TRUE;
      break;
    case 'd':
      dissect = TRUE;
      break;
    case 'b':
      print_branchlen = TRUE;
      break;
    case 'D':
      print_distance_to_root = TRUE;
      node_distance_name = optarg;
      break;
    case 'R':
      reroot_name = optarg;
      break;
    case 'B':
      with_branch = TRUE;
      break;
    case 'a':
      name_ancestors = TRUE;
      break;
    case 'S':
      subtree_name = optarg;
      break;
    case 'n':
      inNewick=TRUE;
      break;
    case 'L':  //do the same for --label--subtree and --label-branches
    case 'l':
      if (label == NULL) {
	label = lst_new_ptr(1);
	labelType = lst_new_int(1);
      }
      optstr = str_new_charstr(optarg);
      lst_push_ptr(label, optstr);
      lst_push_int(labelType, (int)c);
      break;
    case 'h':
      usage(argv[0]);
    case '?':
      die("Bad argument.  Try '%s -h'.\n", argv[0]);
    }
  }

  if (optind != argc - 1) 
    die("Input filename required.  Try '%s -h'.\n", argv[0]);

  if (merge_tree != NULL && extrapolate_tree != NULL)
    die("ERROR: Can't use --merge and --extrapolate together");

  set_seed(-1);
    
  suffix = str_new_charstr(argv[optind]);
  str_suffix(suffix, '.');
  if (inNewick || str_equals_charstr(suffix, "nh")) {
    tree = tr_new_from_file(phast_fopen(argv[optind], "r"));
    tree_only = TRUE;           /* can't output tree model in this case */
  }
  else {
    mod = tm_new_from_file(phast_fopen(argv[optind], "r"), 1);
    tree = mod->tree;
  }

  if (prune_names != NULL) {
    tr_prune(&tree, prune_names, prune_all_but, NULL);
    if (mod != NULL) mod->tree = tree; /* root may have changed */
  }

  if (get_subtree_name != NULL) {
    n = tr_get_node(tree, get_subtree_name);
    if (n == NULL) {
      tr_name_ancestors(tree);
      n = tr_get_node(tree, get_subtree_name);
      if (n == NULL) {
	die("ERROR: no node named '%s'.\n", subtree_name);
      }
    }
    tr_prune_supertree(&tree, n);
    if (mod != NULL) mod->tree = tree;
  }

  if (merge_tree != NULL) {
    tree = tr_hybrid(tree, merge_tree);
    if (mod != NULL) mod->tree = tree;
  }

  else if (extrapolate_tree != NULL) {
    tr_scale_by_subtree(extrapolate_tree, tree);
    tree = extrapolate_tree;
    if (mod != NULL) mod->tree = tree;
  }

  if (scale_factor != 1) {
    if (subtree_name == NULL)
      tr_scale(tree, scale_factor);
    else {
      n = tr_get_node(tree, subtree_name);
      if (n == NULL) die("ERROR: no node named '%s'.\n", subtree_name);
      tr_scale_subtree(tree, n, scale_factor, with_branch);
    }
  }

  if (name_ancestors)
    tr_name_ancestors(tree);

  if (rename_hash != NULL) {
    char *newname;
    for (i = 0; i < tree->nnodes; i++) {
      n = lst_get_ptr(tree->nodes, i);
      if (n->name != NULL && n->name[0] != '\0' && 
          (newname = hsh_get(rename_hash, n->name)) != (char*)-1) {
        strcpy(n->name, newname);
      }
    }
  }

  if (reroot_name != NULL) {
    n = tr_get_node(tree, reroot_name);
    if (n == NULL) die("ERROR: no node named '%s'.\n", reroot_name);
    tr_reroot(tree, n, with_branch);
    if (mod != NULL) mod->tree = with_branch ? n->parent : n;
    tree = with_branch ? n->parent : n;
  }

  if (label != NULL) {
    for (i=0; i < lst_size(label); i++) {
      String *currstr = (String*)lst_get_ptr(label, i), *arg1, *labelVal;
      List *tmplst = lst_new_ptr(10);
      String *nodename;
      int j;
      str_split(currstr, ":", tmplst);
      if (lst_size(tmplst) != 2) 
	die("ERROR: bad argument to --label-branches or --label-subtree.\n");
      arg1 = lst_get_ptr(tmplst, 0);
      labelVal = lst_get_ptr(tmplst, 1);
      lst_clear(tmplst);
      if (lst_get_int(labelType, i) == (int)'l') {
	str_split(arg1, ",", tmplst);
	for (j=0; j < lst_size(tmplst); j++) {
	  nodename = (String*)lst_get_ptr(tmplst, j);
	  tr_label_node(tree, nodename->chars, labelVal->chars);
	}
	lst_free_strings(tmplst);
      } else if (lst_get_int(labelType, i) == (int)'L') {
	int include_leading_branch = FALSE;
	TreeNode *node;
	nodename = arg1;
	node = tr_get_node(tree, nodename->chars);
	if (node == NULL && nodename->chars[nodename->length-1] == '+') {
	  nodename->chars[--nodename->length] = '\0';
	  node = tr_get_node(tree, nodename->chars);
	  include_leading_branch = TRUE;
	}
	tr_label_subtree(tree, nodename->chars, include_leading_branch, 
			 labelVal->chars);
      } else die("ERROR got label_type %c\n", lst_get_int(labelType, (char)i));
      str_free(arg1);
      str_free(labelVal);
      lst_free(tmplst);
      str_free(currstr);
    }
    lst_free(label);
    lst_free(labelType);
  }

  if (dissect) 
    tr_print_nodes(stdout, tree);
  if (print_branchlen) 
    printf("TOTAL_TREE_LEN: %f\n", tr_total_len(tree));
  if (print_distance_to_root) {
    TreeNode *node = tr_get_node(tree, node_distance_name);
    if (node == NULL) 
      die("ERROR: no node named '%s'.\n", node_distance_name);
    printf("length(root-%s): %f\n", node_distance_name, 
	   tr_distance_to_root(node));
  }

  if (dissect==0 && print_branchlen==0 && print_distance_to_root==0) {
    if (tree_only)
      tr_print(stdout, tree, no_branchlen==FALSE);
    else
      tm_print(stdout, mod);
  }
  return 0;
}