treesak 1.51.2__py3-none-any.whl

TreeSAK/RootTreeGTDB220.py

@@ -0,0 +1,300 @@
+import random
+import dendropy
+import argparse
+from ete3 import Tree
+
+
+RootTreeGTDB220_usage = '''
+========================================== RootTreeGTDB220 example command ==========================================   
+
+TreeSAK RootTreeGTDB220 -add_root -d ar -tree ar53.tree -tax ar53.summary.tsv -db db_dir -o ar53.rooted.tree
+TreeSAK RootTreeGTDB220 -add_root -d bac -tree bac120.tree -tax bac120.summary.tsv -db db_dir -o bac120.rooted.tree
+
+# Need to download and decompress the following files to your database folder (provide with -db)
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/ar53_r220.tree.tar.gz
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/bac120_r220.tree.tar.gz
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/ar53_metadata_r220.tsv.gz
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/bac120_metadata_r220.tsv.gz
+
+=====================================================================================================================
+'''
+
+
+def get_smallest_outgroup(tree_object):
+
+    min_outgroup_leaf_num = 99999
+    for each_root_child in tree_object.children:
+        leaf_list = each_root_child.get_leaf_names()
+        if len(leaf_list) < min_outgroup_leaf_num:
+            min_outgroup_leaf_num = len(leaf_list)
+
+    out_group_leaf_list = []
+    for each_root_child in tree_object.children:
+        leaf_list = each_root_child.get_leaf_names()
+        if len(leaf_list) == min_outgroup_leaf_num:
+            out_group_leaf_list = leaf_list
+
+    return out_group_leaf_list
+
+
+def sep_taxon_str(taxon_string):
+
+    taxon_string_split = taxon_string.strip().split(';')
+    taxon_p = taxon_string_split[1]
+    taxon_c = taxon_string_split[2]
+    taxon_o = taxon_string_split[3]
+    taxon_f = taxon_string_split[4]
+    taxon_g = taxon_string_split[5]
+
+    return taxon_p, taxon_c, taxon_o, taxon_f, taxon_g
+
+
+def subset_and_rename_tree(tree_file_in, to_keep_leaf_list, rename_dict):
+
+    input_tree = Tree(tree_file_in, quoted_node_names=True, format=1)
+
+    # subset tree
+    subset_tree = input_tree.copy()
+    subset_tree.prune(to_keep_leaf_list, preserve_branch_length=True)
+
+    # rename leaf
+    for each_leaf in subset_tree:
+        leaf_name_new = rename_dict.get(each_leaf.name, each_leaf.name)
+        each_leaf.name = leaf_name_new
+
+    return subset_tree
+
+
+def root_with_outgroup(input_tree, out_group_list, add_root_branch, tree_file_rooted):
+
+    """
+    Reroot the tree using the given outgroup.
+    modified based on: https://github.com/Ecogenomics/GTDBTk/blob/master/gtdbtk/reroot_tree.py
+
+    input_tree:  File containing Newick tree to rerooted.
+    output_tree: Name of file for rerooted tree.
+    outgroup:    Labels of taxa in outgroup.
+    """
+
+    tree = dendropy.Tree.get_from_path(input_tree, schema='newick', rooting='force-rooted', preserve_underscores=True)
+
+    outgroup_in_tree = set()
+    ingroup_leaves = set()
+    for n in tree.leaf_node_iter():
+        if n.taxon.label in out_group_list:
+            outgroup_in_tree.add(n.taxon)
+        else:
+            ingroup_leaves.add(n)
+
+    # Since finding the MRCA is a rooted tree operation, the tree is first rerooted on an ingroup taxa. This
+    # ensures the MRCA of the outgroup can be identified so long as the outgroup is monophyletic. If the
+    # outgroup is polyphyletic trying to root on it is ill-defined. To try and pick a "good" root for
+    # polyphyletic outgroups, random ingroup taxa are selected until two of them give the same size
+    # lineage. This will, likely, be the smallest bipartition possible for the given outgroup though
+    # this is not guaranteed.
+
+    mrca = tree.mrca(taxa=outgroup_in_tree)
+    mrca_leaves = len(mrca.leaf_nodes())
+    while True:
+        rnd_ingroup = random.sample(list(ingroup_leaves), 1)[0]
+        tree.reroot_at_edge(rnd_ingroup.edge, length1=0.5 * rnd_ingroup.edge_length, length2=0.5 * rnd_ingroup.edge_length)
+        mrca = tree.mrca(taxa=outgroup_in_tree)
+        if len(mrca.leaf_nodes()) == mrca_leaves:
+            break
+        mrca_leaves = len(mrca.leaf_nodes())
+
+    if mrca.edge_length is not None:
+        tree.reroot_at_edge(mrca.edge, length1=0.5 * mrca.edge_length, length2=0.5 * mrca.edge_length)
+
+        # tree.write_to_path(tree_file_rooted, schema='newick', suppress_rooting=True, unquoted_underscores=True)
+        tree_out_string = tree.as_string(schema='newick', suppress_rooting=True, unquoted_underscores=True)
+        tree_out_string = tree_out_string.replace("'", "")
+
+        # add the root bar
+        if add_root_branch is True:
+            tree_out_string = '(' + tree_out_string
+            tree_out_string = tree_out_string.replace(');', '):0.02);')
+
+        # write out tree string
+        tree_file_rooted_handle = open(tree_file_rooted, 'w')
+        tree_file_rooted_handle.write(tree_out_string)
+        tree_file_rooted_handle.close()
+
+
+def RootTreeGTDB220(args):
+
+    input_unrooted_tree = args['tree']
+    user_gnm_taxon      = args['tax']
+    db_dir              = args['db']
+    gnm_domain          = args['d']
+    add_root_branch     = args['add_root']
+    rooted_tree         = args['o']
+
+    leaf_list = []
+    for leaf in Tree(input_unrooted_tree, format=1):
+        leaf_name = leaf.name
+        leaf_list.append(leaf_name)
+
+    # define file name
+    gtdb_ref_tree_ar    = '%s/ar53_r220.tree'           % db_dir
+    gtdb_ref_tree_bac   = '%s/bac120_r220.tree'         % db_dir
+    gtdb_gnm_meta_ar    = '%s/ar53_metadata_r220.tsv'   % db_dir
+    gtdb_gnm_meta_bac   = '%s/bac120_metadata_r220.tsv' % db_dir
+
+    if gnm_domain == 'bac':
+        gtdb_ref_tree = gtdb_ref_tree_bac
+        gtdb_gnm_metadata = gtdb_gnm_meta_bac
+    elif gnm_domain == 'ar':
+        gtdb_ref_tree = gtdb_ref_tree_ar
+        gtdb_gnm_metadata = gtdb_gnm_meta_ar
+    else:
+        print('please provide either "ar" or "bac" to -d')
+        exit()
+
+    tree = Tree(gtdb_ref_tree, quoted_node_names=True, format=1)
+    ref_tree_gnm_list = tree.get_leaf_names()
+    ref_tree_gnm_set = {i for i in ref_tree_gnm_list}
+
+    # read in user_gnm_taxon
+    user_gnm_taxon_dict_p = dict()
+    user_gnm_taxon_dict_c = dict()
+    user_gnm_taxon_dict_o = dict()
+    user_gnm_taxon_dict_f = dict()
+    user_gnm_taxon_dict_g = dict()
+    for each_gnm in open(user_gnm_taxon):
+        if not each_gnm.startswith('user_genome\t'):
+            each_gnm_split = each_gnm.strip().split('\t')
+            gnm_id = each_gnm_split[0]
+            gnm_taxon = each_gnm_split[1]
+
+            if gnm_id in leaf_list:
+                count_current_gnm = False
+                if gnm_domain == 'bac':
+                    if 'd__Bacteria' in gnm_taxon:
+                        count_current_gnm = True
+                elif gnm_domain == 'ar':
+                    if 'd__Archaea' in gnm_taxon:
+                        count_current_gnm = True
+
+                if count_current_gnm is True:
+                    gnm_p, gnm_c, gnm_o, gnm_f, gnm_g = sep_taxon_str(gnm_taxon)
+
+                    if gnm_p not in user_gnm_taxon_dict_p:
+                        user_gnm_taxon_dict_p[gnm_p] = set()
+                    if gnm_c not in user_gnm_taxon_dict_c:
+                        user_gnm_taxon_dict_c[gnm_c] = set()
+                    if gnm_o not in user_gnm_taxon_dict_o:
+                        user_gnm_taxon_dict_o[gnm_o] = set()
+                    if gnm_f not in user_gnm_taxon_dict_f:
+                        user_gnm_taxon_dict_f[gnm_f] = set()
+                    if gnm_g not in user_gnm_taxon_dict_g:
+                        user_gnm_taxon_dict_g[gnm_g] = set()
+
+                    user_gnm_taxon_dict_p[gnm_p].add(gnm_id)
+                    user_gnm_taxon_dict_c[gnm_c].add(gnm_id)
+                    user_gnm_taxon_dict_o[gnm_o].add(gnm_id)
+                    user_gnm_taxon_dict_f[gnm_f].add(gnm_id)
+                    user_gnm_taxon_dict_g[gnm_g].add(gnm_id)
+
+    # determine rooting rank, start from phylum
+    rooting_rank = ''
+    rooting_rank_taxon_dict = dict()
+    if len(user_gnm_taxon_dict_p) > 1:
+        rooting_rank = 'p'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_p
+    elif len(user_gnm_taxon_dict_c) > 1:
+        rooting_rank = 'c'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_c
+    elif len(user_gnm_taxon_dict_o) > 1:
+        rooting_rank = 'o'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_o
+    elif len(user_gnm_taxon_dict_f) > 1:
+        rooting_rank = 'f'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_f
+    elif len(user_gnm_taxon_dict_g) > 1:
+        rooting_rank = 'g'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_g
+
+    if rooting_rank == '':
+        print('All user genomes are from the same genus, program exited!')
+        exit()
+
+    col_index = {}
+    canditate_gnms_rooting_rank = dict()
+    counted_taxons_rooting_rank = set()
+    for each_ref in open(gtdb_gnm_metadata):
+            each_ref_split = each_ref.strip().split('\t')
+            if each_ref.startswith('accession	ambiguous_bases'):
+                col_index = {key: i for i, key in enumerate(each_ref_split)}
+            else:
+                ref_accession = each_ref_split[0]
+                gtdb_taxonomy = each_ref_split[col_index['gtdb_taxonomy']]
+                if ref_accession in ref_tree_gnm_set:
+                    gnm_p, gnm_c, gnm_o, gnm_f, gnm_g = sep_taxon_str(gtdb_taxonomy)
+
+                    gnm_rooting_rank = ''
+                    if rooting_rank == 'p':
+                        gnm_rooting_rank = gnm_p
+                    elif rooting_rank == 'c':
+                        gnm_rooting_rank = gnm_c
+                    elif rooting_rank == 'o':
+                        gnm_rooting_rank = gnm_o
+                    elif rooting_rank == 'f':
+                        gnm_rooting_rank = gnm_f
+                    elif rooting_rank == 'g':
+                        gnm_rooting_rank = gnm_g
+
+                    # rooting_rank
+                    if gnm_rooting_rank in rooting_rank_taxon_dict:
+                        if gnm_rooting_rank not in counted_taxons_rooting_rank:
+                            counted_taxons_rooting_rank.add(gnm_rooting_rank)
+                            canditate_gnms_rooting_rank[ref_accession] = gnm_rooting_rank
+
+    ref_tree_rooting_rank = subset_and_rename_tree(gtdb_ref_tree, canditate_gnms_rooting_rank, canditate_gnms_rooting_rank)
+
+    # get the smallest out group taxon set
+    smallest_outgroup_taxon_list = get_smallest_outgroup(ref_tree_rooting_rank)
+
+    user_gnm_taxon_dict_rooting_rank = dict()
+    if rooting_rank == 'p':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_p
+    elif rooting_rank == 'c':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_c
+    elif rooting_rank == 'o':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_o
+    elif rooting_rank == 'f':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_f
+    elif rooting_rank == 'g':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_g
+
+    # get the smallest out group genome set
+    out_group_gnm_set_1 = set()
+    out_group_gnm_set_2 = set()
+    for each_rooting_rank_taxon in user_gnm_taxon_dict_rooting_rank:
+        gnm_member_set = user_gnm_taxon_dict_rooting_rank[each_rooting_rank_taxon]
+        if each_rooting_rank_taxon in smallest_outgroup_taxon_list:
+            out_group_gnm_set_1.update(gnm_member_set)
+        else:
+            out_group_gnm_set_2.update(gnm_member_set)
+
+    # select the smaller one as outgroup
+    if len(out_group_gnm_set_1) < len(out_group_gnm_set_2):
+        out_group_gnm_set = out_group_gnm_set_1
+    else:
+        out_group_gnm_set = out_group_gnm_set_2
+
+    # root user tree with identified out group genomes
+    root_with_outgroup(input_unrooted_tree, out_group_gnm_set, add_root_branch, rooted_tree)
+
+
+if __name__ == '__main__':
+
+    RootTreeGTDB220_parser = argparse.ArgumentParser(usage=RootTreeGTDB220_usage)
+    RootTreeGTDB220_parser.add_argument('-tree',        required=True,                         help='input unrooted tree')
+    RootTreeGTDB220_parser.add_argument('-tax',         required=False, default='fna',         help='leaf taxon')
+    RootTreeGTDB220_parser.add_argument('-db',          required=True,                         help='GTDB database files')
+    RootTreeGTDB220_parser.add_argument('-d',           required=False, default=None,          help='domain, either ar or bac')
+    RootTreeGTDB220_parser.add_argument('-add_root',    required=False, action='store_true',   help='add the root branch')
+    RootTreeGTDB220_parser.add_argument('-o',           required=True,                         help='output folder')
+    args = vars(RootTreeGTDB220_parser.parse_args())
+    RootTreeGTDB220(args)

TreeSAK/RootTreeGTDB226.py

@@ -0,0 +1,300 @@
+import random
+import dendropy
+import argparse
+from ete3 import Tree
+
+
+RootTreeGTDB226_usage = '''
+========================================== RootTreeGTDB226 example command ==========================================   
+
+TreeSAK RootTreeGTDB226 -add_root -d ar -tree ar53.tree -tax ar53.summary.tsv -db db_dir -o ar53.rooted.tree
+TreeSAK RootTreeGTDB226 -add_root -d bac -tree bac120.tree -tax bac120.summary.tsv -db db_dir -o bac120.rooted.tree
+
+# Need to download and decompress the following files to your database folder (provide with -db)
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/ar53_r226.tree.tar.gz
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/bac120_r226.tree.tar.gz
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/ar53_metadata_r226.tsv.gz
+https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/bac120_metadata_r226.tsv.gz
+
+=====================================================================================================================
+'''
+
+
+def get_smallest_outgroup(tree_object):
+
+    min_outgroup_leaf_num = 99999
+    for each_root_child in tree_object.children:
+        leaf_list = each_root_child.get_leaf_names()
+        if len(leaf_list) < min_outgroup_leaf_num:
+            min_outgroup_leaf_num = len(leaf_list)
+
+    out_group_leaf_list = []
+    for each_root_child in tree_object.children:
+        leaf_list = each_root_child.get_leaf_names()
+        if len(leaf_list) == min_outgroup_leaf_num:
+            out_group_leaf_list = leaf_list
+
+    return out_group_leaf_list
+
+
+def sep_taxon_str(taxon_string):
+
+    taxon_string_split = taxon_string.strip().split(';')
+    taxon_p = taxon_string_split[1]
+    taxon_c = taxon_string_split[2]
+    taxon_o = taxon_string_split[3]
+    taxon_f = taxon_string_split[4]
+    taxon_g = taxon_string_split[5]
+
+    return taxon_p, taxon_c, taxon_o, taxon_f, taxon_g
+
+
+def subset_and_rename_tree(tree_file_in, to_keep_leaf_list, rename_dict):
+
+    input_tree = Tree(tree_file_in, quoted_node_names=True, format=1)
+
+    # subset tree
+    subset_tree = input_tree.copy()
+    subset_tree.prune(to_keep_leaf_list, preserve_branch_length=True)
+
+    # rename leaf
+    for each_leaf in subset_tree:
+        leaf_name_new = rename_dict.get(each_leaf.name, each_leaf.name)
+        each_leaf.name = leaf_name_new
+
+    return subset_tree
+
+
+def root_with_outgroup(input_tree, out_group_list, add_root_branch, tree_file_rooted):
+
+    """
+    Reroot the tree using the given outgroup.
+    modified based on: https://github.com/Ecogenomics/GTDBTk/blob/master/gtdbtk/reroot_tree.py
+
+    input_tree:  File containing Newick tree to rerooted.
+    output_tree: Name of file for rerooted tree.
+    outgroup:    Labels of taxa in outgroup.
+    """
+
+    tree = dendropy.Tree.get_from_path(input_tree, schema='newick', rooting='force-rooted', preserve_underscores=True)
+
+    outgroup_in_tree = set()
+    ingroup_leaves = set()
+    for n in tree.leaf_node_iter():
+        if n.taxon.label in out_group_list:
+            outgroup_in_tree.add(n.taxon)
+        else:
+            ingroup_leaves.add(n)
+
+    # Since finding the MRCA is a rooted tree operation, the tree is first rerooted on an ingroup taxa. This
+    # ensures the MRCA of the outgroup can be identified so long as the outgroup is monophyletic. If the
+    # outgroup is polyphyletic trying to root on it is ill-defined. To try and pick a "good" root for
+    # polyphyletic outgroups, random ingroup taxa are selected until two of them give the same size
+    # lineage. This will, likely, be the smallest bipartition possible for the given outgroup though
+    # this is not guaranteed.
+
+    mrca = tree.mrca(taxa=outgroup_in_tree)
+    mrca_leaves = len(mrca.leaf_nodes())
+    while True:
+        rnd_ingroup = random.sample(list(ingroup_leaves), 1)[0]
+        tree.reroot_at_edge(rnd_ingroup.edge, length1=0.5 * rnd_ingroup.edge_length, length2=0.5 * rnd_ingroup.edge_length)
+        mrca = tree.mrca(taxa=outgroup_in_tree)
+        if len(mrca.leaf_nodes()) == mrca_leaves:
+            break
+        mrca_leaves = len(mrca.leaf_nodes())
+
+    if mrca.edge_length is not None:
+        tree.reroot_at_edge(mrca.edge, length1=0.5 * mrca.edge_length, length2=0.5 * mrca.edge_length)
+
+        # tree.write_to_path(tree_file_rooted, schema='newick', suppress_rooting=True, unquoted_underscores=True)
+        tree_out_string = tree.as_string(schema='newick', suppress_rooting=True, unquoted_underscores=True)
+        tree_out_string = tree_out_string.replace("'", "")
+
+        # add the root bar
+        if add_root_branch is True:
+            tree_out_string = '(' + tree_out_string
+            tree_out_string = tree_out_string.replace(');', '):0.02);')
+
+        # write out tree string
+        tree_file_rooted_handle = open(tree_file_rooted, 'w')
+        tree_file_rooted_handle.write(tree_out_string)
+        tree_file_rooted_handle.close()
+
+
+def RootTreeGTDB226(args):
+
+    input_unrooted_tree = args['tree']
+    user_gnm_taxon      = args['tax']
+    db_dir              = args['db']
+    gnm_domain          = args['d']
+    add_root_branch     = args['add_root']
+    rooted_tree         = args['o']
+
+    leaf_list = []
+    for leaf in Tree(input_unrooted_tree, format=1):
+        leaf_name = leaf.name
+        leaf_list.append(leaf_name)
+
+    # define file name
+    gtdb_ref_tree_ar    = '%s/ar53_r226.tree'           % db_dir
+    gtdb_ref_tree_bac   = '%s/bac120_r226.tree'         % db_dir
+    gtdb_gnm_meta_ar    = '%s/ar53_metadata_r226.tsv'   % db_dir
+    gtdb_gnm_meta_bac   = '%s/bac120_metadata_r226.tsv' % db_dir
+
+    if gnm_domain == 'bac':
+        gtdb_ref_tree = gtdb_ref_tree_bac
+        gtdb_gnm_metadata = gtdb_gnm_meta_bac
+    elif gnm_domain == 'ar':
+        gtdb_ref_tree = gtdb_ref_tree_ar
+        gtdb_gnm_metadata = gtdb_gnm_meta_ar
+    else:
+        print('please provide either "ar" or "bac" to -d')
+        exit()
+
+    tree = Tree(gtdb_ref_tree, quoted_node_names=True, format=1)
+    ref_tree_gnm_list = tree.get_leaf_names()
+    ref_tree_gnm_set = {i for i in ref_tree_gnm_list}
+
+    # read in user_gnm_taxon
+    user_gnm_taxon_dict_p = dict()
+    user_gnm_taxon_dict_c = dict()
+    user_gnm_taxon_dict_o = dict()
+    user_gnm_taxon_dict_f = dict()
+    user_gnm_taxon_dict_g = dict()
+    for each_gnm in open(user_gnm_taxon):
+        if not each_gnm.startswith('user_genome\t'):
+            each_gnm_split = each_gnm.strip().split('\t')
+            gnm_id = each_gnm_split[0]
+            gnm_taxon = each_gnm_split[1]
+
+            if gnm_id in leaf_list:
+                count_current_gnm = False
+                if gnm_domain == 'bac':
+                    if 'd__Bacteria' in gnm_taxon:
+                        count_current_gnm = True
+                elif gnm_domain == 'ar':
+                    if 'd__Archaea' in gnm_taxon:
+                        count_current_gnm = True
+
+                if count_current_gnm is True:
+                    gnm_p, gnm_c, gnm_o, gnm_f, gnm_g = sep_taxon_str(gnm_taxon)
+
+                    if gnm_p not in user_gnm_taxon_dict_p:
+                        user_gnm_taxon_dict_p[gnm_p] = set()
+                    if gnm_c not in user_gnm_taxon_dict_c:
+                        user_gnm_taxon_dict_c[gnm_c] = set()
+                    if gnm_o not in user_gnm_taxon_dict_o:
+                        user_gnm_taxon_dict_o[gnm_o] = set()
+                    if gnm_f not in user_gnm_taxon_dict_f:
+                        user_gnm_taxon_dict_f[gnm_f] = set()
+                    if gnm_g not in user_gnm_taxon_dict_g:
+                        user_gnm_taxon_dict_g[gnm_g] = set()
+
+                    user_gnm_taxon_dict_p[gnm_p].add(gnm_id)
+                    user_gnm_taxon_dict_c[gnm_c].add(gnm_id)
+                    user_gnm_taxon_dict_o[gnm_o].add(gnm_id)
+                    user_gnm_taxon_dict_f[gnm_f].add(gnm_id)
+                    user_gnm_taxon_dict_g[gnm_g].add(gnm_id)
+
+    # determine rooting rank, start from phylum
+    rooting_rank = ''
+    rooting_rank_taxon_dict = dict()
+    if len(user_gnm_taxon_dict_p) > 1:
+        rooting_rank = 'p'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_p
+    elif len(user_gnm_taxon_dict_c) > 1:
+        rooting_rank = 'c'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_c
+    elif len(user_gnm_taxon_dict_o) > 1:
+        rooting_rank = 'o'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_o
+    elif len(user_gnm_taxon_dict_f) > 1:
+        rooting_rank = 'f'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_f
+    elif len(user_gnm_taxon_dict_g) > 1:
+        rooting_rank = 'g'
+        rooting_rank_taxon_dict = user_gnm_taxon_dict_g
+
+    if rooting_rank == '':
+        print('All user genomes are from the same genus, program exited!')
+        exit()
+
+    col_index = {}
+    canditate_gnms_rooting_rank = dict()
+    counted_taxons_rooting_rank = set()
+    for each_ref in open(gtdb_gnm_metadata):
+            each_ref_split = each_ref.strip().split('\t')
+            if each_ref.startswith('accession	ambiguous_bases'):
+                col_index = {key: i for i, key in enumerate(each_ref_split)}
+            else:
+                ref_accession = each_ref_split[0]
+                gtdb_taxonomy = each_ref_split[col_index['gtdb_taxonomy']]
+                if ref_accession in ref_tree_gnm_set:
+                    gnm_p, gnm_c, gnm_o, gnm_f, gnm_g = sep_taxon_str(gtdb_taxonomy)
+
+                    gnm_rooting_rank = ''
+                    if rooting_rank == 'p':
+                        gnm_rooting_rank = gnm_p
+                    elif rooting_rank == 'c':
+                        gnm_rooting_rank = gnm_c
+                    elif rooting_rank == 'o':
+                        gnm_rooting_rank = gnm_o
+                    elif rooting_rank == 'f':
+                        gnm_rooting_rank = gnm_f
+                    elif rooting_rank == 'g':
+                        gnm_rooting_rank = gnm_g
+
+                    # rooting_rank
+                    if gnm_rooting_rank in rooting_rank_taxon_dict:
+                        if gnm_rooting_rank not in counted_taxons_rooting_rank:
+                            counted_taxons_rooting_rank.add(gnm_rooting_rank)
+                            canditate_gnms_rooting_rank[ref_accession] = gnm_rooting_rank
+
+    ref_tree_rooting_rank = subset_and_rename_tree(gtdb_ref_tree, canditate_gnms_rooting_rank, canditate_gnms_rooting_rank)
+
+    # get the smallest out group taxon set
+    smallest_outgroup_taxon_list = get_smallest_outgroup(ref_tree_rooting_rank)
+
+    user_gnm_taxon_dict_rooting_rank = dict()
+    if rooting_rank == 'p':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_p
+    elif rooting_rank == 'c':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_c
+    elif rooting_rank == 'o':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_o
+    elif rooting_rank == 'f':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_f
+    elif rooting_rank == 'g':
+        user_gnm_taxon_dict_rooting_rank = user_gnm_taxon_dict_g
+
+    # get the smallest out group genome set
+    out_group_gnm_set_1 = set()
+    out_group_gnm_set_2 = set()
+    for each_rooting_rank_taxon in user_gnm_taxon_dict_rooting_rank:
+        gnm_member_set = user_gnm_taxon_dict_rooting_rank[each_rooting_rank_taxon]
+        if each_rooting_rank_taxon in smallest_outgroup_taxon_list:
+            out_group_gnm_set_1.update(gnm_member_set)
+        else:
+            out_group_gnm_set_2.update(gnm_member_set)
+
+    # select the smaller one as outgroup
+    if len(out_group_gnm_set_1) < len(out_group_gnm_set_2):
+        out_group_gnm_set = out_group_gnm_set_1
+    else:
+        out_group_gnm_set = out_group_gnm_set_2
+
+    # root user tree with identified out group genomes
+    root_with_outgroup(input_unrooted_tree, out_group_gnm_set, add_root_branch, rooted_tree)
+
+
+if __name__ == '__main__':
+
+    RootTreeGTDB226_parser = argparse.ArgumentParser(usage=RootTreeGTDB226_usage)
+    RootTreeGTDB226_parser.add_argument('-tree',        required=True,                         help='input unrooted tree')
+    RootTreeGTDB226_parser.add_argument('-tax',         required=False, default='fna',         help='leaf taxon')
+    RootTreeGTDB226_parser.add_argument('-db',          required=True,                         help='GTDB database files')
+    RootTreeGTDB226_parser.add_argument('-d',           required=False, default=None,          help='domain, either ar or bac')
+    RootTreeGTDB226_parser.add_argument('-add_root',    required=False, action='store_true',   help='add the root branch')
+    RootTreeGTDB226_parser.add_argument('-o',           required=True,                         help='output folder')
+    args = vars(RootTreeGTDB226_parser.parse_args())
+    RootTreeGTDB226(args)

TreeSAK/SequentialDating.py

@@ -0,0 +1,16 @@
+
+SequentialDating_usage = '''
+======================== SequentialDating example commands ========================
+
+TreeSAK SequentialDating -h
+
+===================================================================================
+'''
+
+
+def SequentialDating():
+
+    pass
+
+
+SequentialDating()