treesak 1.53.3__py3-none-any.whl

TreeSAK/parse_mcmctree.py

@@ -0,0 +1,198 @@
+import os
+import glob
+import argparse
+from ete3 import Tree
+
+
+VisHPD95_usage = '''
+============================ VisHPD95 example command ============================
+
+TreeSAK VisHPD95 -i mcmc_out -o HPD95.pdf -n nodes.txt -label label.txt
+TreeSAK VisHPD95 -i mcmc_out -o HPD95.pdf -n nodes.txt -label label.txt -x 9 -y 6
+
+# Example data
+https://github.com/songweizhi/TreeSAK/tree/master/example_data/VisHPD95
+
+==================================================================================
+'''
+
+def mcmctree_out_to_tree_str(mamctree_out):
+
+    # get tree string from mamctree_out
+    tree_str = ''
+    tree_line = 0
+    current_line = 1
+    for each_line in open(mamctree_out):
+        if 'Species tree for FigTree.  Branch lengths = posterior mean times; 95% CIs = labels' in each_line:
+            tree_line = current_line + 1
+        if tree_line == current_line:
+            tree_str = each_line.strip()
+        current_line += 1
+
+    tree_str_no_space = tree_str.replace(' ', '')
+
+    # rename tree nodes
+    t = Tree(tree_str_no_space, format=1)
+    for each_node in t.traverse():
+        if each_node.is_leaf():
+            node_name_new = '_'.join(each_node.name.split('_')[1:])
+        else:
+            node_name_new = 't_n%s' % each_node.name
+        each_node.name = node_name_new
+
+    tree_str_renamed = t.write(format=8)
+
+    return tree_str_renamed
+
+
+def get_internal_node_to_plot(node_txt, mo_file):
+
+    tree_str = ''
+    if os.path.isfile(mo_file):
+        tree_str = mcmctree_out_to_tree_str(mo_file)
+
+    # get nodes to plot
+    node_set = set()
+    node_rename_dict = dict()
+    if os.path.isfile(node_txt) is True:
+        for each in open(node_txt):
+            each_split = each.strip().split('\t')
+            node_str = each_split[0]
+
+            # get internal_node_to_plot
+            internal_node_to_plot = ''
+            if ',' not in node_str:
+                internal_node_to_plot = each_split[0]
+            else:
+                leaf_list = node_str.split(',')
+                if tree_str == '':
+                    print('MCMCTree out file not found, program exited!')
+                    exit()
+                current_lca = Tree(tree_str, format=1).get_common_ancestor(leaf_list)
+                internal_node_to_plot = current_lca.name
+
+            # add internal_node_to_plot to  node_set
+            if internal_node_to_plot != '':
+                node_set.add(internal_node_to_plot)
+
+            # read in name to show in plot
+            if len(each_split) == 2:
+                if each_split[1] != '':
+                    node_rename_dict[internal_node_to_plot] = each_split[1]
+    else:
+        node_set = node_txt.split(',')
+
+    return node_set, node_rename_dict, tree_str
+
+
+def read_in_posterior_mean(mcmctree_out):
+
+    # read in Posterior mean
+    node_to_mean_hpd95_dict = dict()
+    current_line = 1
+    posterior_mean_header_line = 0
+    for each_line in open(mcmctree_out):
+        if 'Posterior mean (95% Equal-tail CI) (95% HPD CI) HPD-CI-width' in each_line:
+            posterior_mean_header_line = current_line
+
+        if (posterior_mean_header_line != 0) and (current_line > posterior_mean_header_line):
+            each_line_split = each_line.strip().split(' ')
+
+            each_line_split_no_empty = []
+            for each_element in each_line_split:
+                if each_element not in ['', '(']:
+                    each_element_value = each_element.replace('(', '').replace(')', '').replace(',', '')
+                    each_line_split_no_empty.append(each_element_value)
+            if len(each_line_split_no_empty) == 9:
+                node_id           = each_line_split_no_empty[0]
+                value_mean        = each_line_split_no_empty[1]
+                value_hpd95_small = each_line_split_no_empty[4]
+                value_hpd95_big   = each_line_split_no_empty[5]
+                node_to_mean_hpd95_dict[node_id] = [value_mean, value_hpd95_small, value_hpd95_big]
+        current_line += 1
+
+    return node_to_mean_hpd95_dict
+
+
+def VisHPD95(args):
+
+    mcmc_in     = args['i']
+    node_txt    = args['n']
+    label_txt   = args['label']
+    plot_out    = args['o']
+    plot_width  = args['x']
+    plot_height = args['y']
+
+    pwd_current_file  = os.path.realpath(__file__)
+    current_file_path = '/'.join(pwd_current_file.split('/')[:-1])
+    VisHPD95_R  = '%s/VisHPD95.R' % current_file_path
+
+    dm_out      = '%s.txt' % plot_out
+
+    # check MCMCTree output file/dir
+    if os.path.isfile(mcmc_in) is True:
+        mcmc_out_file_list = [mcmc_in]
+    else:
+        mcmc_out_file_re = '%s/*_out.txt' % (mcmc_in)
+        mcmc_out_file_list = glob.glob(mcmc_out_file_re)
+
+    if len(mcmc_out_file_list) == 0:
+        print('MCMCTree out file not found, program exited!')
+        exit()
+
+    # read in y-axis label file
+    label_dict = dict()
+    color_dict = dict()
+    shape_dict = dict()
+    if label_txt is not None:
+        for each_sample in open(label_txt):
+            each_sample_split = each_sample.strip().split('\t')
+            if len(each_sample_split) == 3:
+                label_dict[each_sample_split[0]] = each_sample_split[1]
+                color_dict[each_sample_split[0]] = each_sample_split[1]
+                shape_dict[each_sample_split[0]] = each_sample_split[2]
+            else:
+                print('Format error: %s' % label_txt)
+                exit()
+
+    dm_out_handle = open(dm_out, 'w')
+    dm_out_handle.write('Test\tShape\tVar\tMean\tLow\tHigh\n')
+    for mcmc_out_file in mcmc_out_file_list:
+        mcmc_out_file_no_path = mcmc_out_file
+        if '/' in mcmc_out_file_no_path:
+            mcmc_out_file_no_path = mcmc_out_file_no_path.split('/')[-1]
+
+        color_col_to_write = color_dict.get(mcmc_out_file_no_path, mcmc_out_file_no_path)
+        shape_col_to_write = shape_dict.get(mcmc_out_file_no_path, mcmc_out_file_no_path)
+        node_set, node_rename_dict, tree_str = get_internal_node_to_plot(node_txt, mcmc_out_file)
+        node_to_mean_95_hpd_dict = read_in_posterior_mean(mcmc_out_file)
+
+        for each_node in node_set:
+            node_name_to_write = node_rename_dict.get(each_node, each_node)
+            mean_95_hpd_list = node_to_mean_95_hpd_dict.get(each_node)
+            dm_out_handle.write('%s\t%s\t%s\t%s\n' % (color_col_to_write, shape_col_to_write, node_name_to_write, '\t'.join(mean_95_hpd_list)))
+    dm_out_handle.close()
+
+    plot_cmd   = 'Rscript %s -i %s -x %s -y %s -o %s' % (VisHPD95_R, dm_out, plot_width, plot_height, plot_out)
+    os.system(plot_cmd)
+    print('Plot exported to: %s' % plot_out)
+
+
+if __name__ == '__main__':
+
+    VisHPD95_parser = argparse.ArgumentParser()
+    VisHPD95_parser.add_argument('-i',      required=True,                      help='mcmc.txt file or folder')
+    VisHPD95_parser.add_argument('-n',      required=True,                      help='Nodes to plot')
+    VisHPD95_parser.add_argument('-label',  required=False, default=None,       help='labels on y axis')
+    VisHPD95_parser.add_argument('-x',      required=False, default=8,type=int, help='plot width, default: 8')
+    VisHPD95_parser.add_argument('-y',      required=False, default=5,type=int, help='plot height, default: 5')
+    VisHPD95_parser.add_argument('-o',      required=True,                      help='Output plot')
+    args = vars(VisHPD95_parser.parse_args())
+    VisHPD95(args)
+
+'''
+
+cd /Users/songweizhi/Desktop/777
+python3 ~/PycharmProjects/TreeSAK/TreeSAK/VisHPD95.py -i M1_mcmc_txt -o M1_HPD95.pdf -n nodes_five.txt -label y_label_out.txt
+
+'''

TreeSAK/parse_reltime.py

@@ -0,0 +1,141 @@
+import os
+import argparse
+
+
+parse_reltime_usage = '''
+==================== parse_reltime example commands ====================
+
+TreeSAK parse_reltime -i RelTime.txt -n dbscc_lca.txt -o dbscc_age.txt
+
+========================================================================
+'''
+
+def sep_path_basename_ext(file_in):
+
+    f_path, f_name = os.path.split(file_in)
+    if f_path == '':
+        f_path = '.'
+    f_base, f_ext = os.path.splitext(f_name)
+
+    return f_name, f_path, f_base, f_ext[1:]
+
+
+def get_lca(reltime_txt, leaf_1_name, leaf_2_name):
+
+    leaf_set = set()
+    child_to_parent_dict = dict()
+    id_to_name_dict = dict()
+    name_to_id_dict = dict()
+    for each_line in open(reltime_txt):
+        if not each_line.startswith('NodeLabel'):
+            each_line_split = each_line.strip().split('\t')
+            each_line_split = [i.strip() for i in each_line_split]
+            if len(each_line_split) > 1:
+                node_name = each_line_split[0].replace(' ', '_')
+                node_id = each_line_split[1]
+                des1 = each_line_split[2]
+                des2 = each_line_split[3]
+                id_to_name_dict[node_id] = node_name
+                name_to_id_dict[node_name] = node_id
+                child_to_parent_dict[des1] = node_id
+                child_to_parent_dict[des2] = node_id
+                if (des1 == '-') and (des2 == '-'):
+                    leaf_set.add(node_id)
+
+    leaf_to_lineage_dict = dict()
+    for leaf in sorted([i for i in leaf_set]):
+        original_leaf = leaf
+        lineage_list = [leaf]
+        while leaf in child_to_parent_dict:
+            leaf_p = child_to_parent_dict[leaf]
+            lineage_list.append(leaf_p)
+            leaf = leaf_p
+        leaf_to_lineage_dict[original_leaf] = lineage_list
+
+    leaf_1_id     = name_to_id_dict[leaf_1_name]
+    leaf_2_id     = name_to_id_dict[leaf_2_name]
+    leaf_1_linage = leaf_to_lineage_dict[leaf_1_id]
+    leaf_2_linage = leaf_to_lineage_dict[leaf_2_id]
+
+    lca = ''
+    for each_p in leaf_1_linage[::-1]:
+        if each_p in leaf_2_linage:
+            lca = each_p
+    return lca
+
+
+def parse_reltime(args):
+
+    reltime_txt          = args['i']
+    interested_nodes_txt = args['n']
+    op_txt               = args['o']
+
+    f_name, f_path, f_base, f_ext = sep_path_basename_ext(op_txt)
+    op_txt_all_info = '%s/%s_all_info.%s' % (f_path,f_base, f_ext)
+
+    lca_to_leaves_dict = dict()
+    interested_node_desc_dict = dict()
+    for interested_node in open(interested_nodes_txt):
+        interested_node_split = interested_node.strip().split('\t')
+        paired_leaves = interested_node_split[0]
+        interested_node_desc = paired_leaves
+        if len(interested_node_split) > 1:
+            interested_node_desc = interested_node_split[1]
+        interested_node_desc_dict[paired_leaves] = interested_node_desc
+        leaf_1 = paired_leaves.split(',')[0]
+        leaf_2 = paired_leaves.split(',')[1]
+        lca_id = get_lca(reltime_txt, leaf_1, leaf_2)
+        lca_to_leaves_dict[lca_id] = paired_leaves.strip()
+
+    op_txt_all_info_handle = open(op_txt_all_info, 'w')
+    line_num_index = 0
+    for each_line in open(reltime_txt):
+        each_line_split = each_line.strip().split('\t')
+        each_line_split = [i.strip() for i in each_line_split]
+        if line_num_index == 0:
+            op_txt_all_info_handle.write('Leaves\tDescription\t%s\n' % ('\t'.join(each_line_split)))
+        else:
+            if len(each_line_split) > 1:
+                node_id = each_line_split[1]
+                if node_id in lca_to_leaves_dict:
+                    node_id = each_line_split[1]
+                    corresponding_leaves = lca_to_leaves_dict[node_id]
+                    interested_node_desc = interested_node_desc_dict[corresponding_leaves]
+                    op_txt_all_info_handle.write('%s\t%s\t%s\n' % (corresponding_leaves, interested_node_desc, '\t'.join(each_line_split)))
+        line_num_index += 1
+    op_txt_all_info_handle.close()
+
+    op_txt_handle = open(op_txt, 'w')
+    op_txt_handle.write('Node\tDivTime\tCI_Lower\tCI_Upper\n')
+    line_num_index = 0
+    for each_line in open(op_txt_all_info):
+        if line_num_index > 0:
+            each_line_split = each_line.strip().split('\t')
+            desc = each_line_split[1]
+            div_time = each_line_split[9]
+            ci_lower = each_line_split[10]
+            ci_upper = each_line_split[11]
+            op_txt_handle.write('%s\t%s\t%s\t%s\n' % (desc, div_time, ci_lower, ci_upper))
+        line_num_index += 1
+    op_txt_handle.close()
+
+
+if __name__ == '__main__':
+
+    parse_reltime_parser = argparse.ArgumentParser()
+    parse_reltime_parser.add_argument('-i',  required=True, help='reltime output file')
+    parse_reltime_parser.add_argument('-n',  required=True, help='interested node txt')
+    parse_reltime_parser.add_argument('-o',  required=True, help='output txt file')
+    args = vars(parse_reltime_parser.parse_args())
+    parse_reltime(args)
+
+
+'''
+
+cd /Users/songweizhi/Desktop
+python3 /Users/songweizhi/PycharmProjects/TreeSAK/TreeSAK/parse_reltime.py -i /Users/songweizhi/Desktop/Sponge_r220/6_dating/RelTime/topo2_p30_RelTime_JTT_Gamma4/topo2_p30_RelTime_Gamma4.txt -n yang_7.txt -o dbscc_age.txt
+
+cd /Users/songweizhi/Desktop
+TreeSAK parse_reltime -i /Users/songweizhi/Desktop/Sponge_r220/6_dating/RelTime/topo2_p30_RelTime_JTT_Gamma4/topo2_p30_RelTime_Gamma4.txt -n yang_7.txt -o dbscc_age.txt
+
+'''

TreeSAK/phy2fa.py

@@ -0,0 +1,37 @@
+import argparse
+from Bio import SeqIO
+from Bio import AlignIO
+
+
+phy2fa_usage = '''
+======= phy2fa example commands =======
+
+TreeSAK phy2fa -i msa.phy -o msa.fa
+
+=======================================
+'''
+
+
+def phy2fa(args):
+
+    phylip_in   = args['i']
+    fasta_out   = args['o']
+
+    for aln in AlignIO.parse(phylip_in, "phylip"):
+        print(aln)
+
+    # alignments = list(AlignIO.parse(phylip_in, "phylip"))
+    # print(alignments)
+    # records = SeqIO.parse(phylip_in, "phylip")
+    # count = SeqIO.write(records, fasta_out, "fasta")
+    # print("Converted %i records" % count)
+
+
+if __name__ == '__main__':
+
+    # initialize the options parser
+    phy2fa_parser = argparse.ArgumentParser()
+    phy2fa_parser.add_argument('-i',      required=True,   help='input MSA in phylip format')
+    phy2fa_parser.add_argument('-o',      required=True,   help='output MSA in fasta format')
+    args = vars(phy2fa_parser.parse_args())
+    phy2fa(args)

TreeSAK/plot_distruibution_th.py

@@ -0,0 +1,165 @@
+import io
+import pandas as pd
+from tqdm import tqdm
+from ete3 import Tree
+from glob import glob
+from os.path import *
+import plotly.express as px
+import plotly.graph_objects as go
+import plotly.figure_factory as ff
+
+
+def read_mcmc(mcmc, all_col=False):
+    if type(mcmc) != str:
+        return mcmc
+    if all_col:
+        mcmc_df = pd.read_csv(mcmc, sep='\t', index_col=0)
+    else:
+        f1 = open(mcmc)
+        header = [_ for _ in next(f1).strip().split('\t')]
+        r_header = [_ for _ in header if not _.startswith('r_g')]
+        # normally it need to iterate rows and ignore the columns representing rates
+        text = '\t'.join(r_header) + '\n'
+        r_header = set(r_header)
+        for row in f1:
+            text += '\t'.join([r for r, h in zip(row.strip().split('\t'), header) if h in r_header]) + '\n'
+        mcmc_df = pd.read_csv(io.StringIO(text), sep='\t', index_col=0)
+    return mcmc_df
+
+
+def get_node_name_from_log(f):
+    # f should be the *.log file
+    rows = open(f).read().split('\n')
+    idx = [_ for _, r in enumerate(rows) if r == 'Species tree']
+    if not idx:
+        print("prior not complete")
+        return
+    idx = idx[0]
+    start_idx = idx + 3
+    end_idx = 0
+    for _ in range(idx, 100000):
+        if rows[_] == '':
+            end_idx = _
+            break
+    tree_idx1 = end_idx + 1
+    tree_idx2 = end_idx + 2
+    # find the index
+    n2father = {}
+    for i in range(start_idx, end_idx):
+        row = [_ for _ in rows[i].split(' ') if _]
+        father, n, name = row[0], row[1], row[2]
+        n2father[name if len(row) == 4 else n] = father
+
+    t = Tree(rows[tree_idx2], format=8)
+    for l in t.traverse('postorder'):
+        if l.up is None:
+            break
+        if not l.up.name:
+            l.up.name = n2father[l.name]
+    return t
+
+
+indir                   = '/Users/songweizhi/Desktop/DateArTree/plot_distruibution/stepwise'
+tree_dir                = '/Users/songweizhi/Desktop/DateArTree/plot_distruibution/treefile_dir'
+plot_dir                = '/Users/songweizhi/Desktop/DateArTree/plot_distruibution'
+
+gene_names              = ['M24', 'COG25']
+M24_gene_list           = ['MitoCOG0043', 'MitoCOG0040', 'MitoCOG0055', 'MitoCOG0052', 'MitoCOG0053', 'MitoCOG0133', 'MitoCOG0008', 'MitoCOG0009', 'MitoCOG0027', 'MitoCOG0031', 'MitoCOG0030', 'MitoCOG0001', 'MitoCOG0003', 'MitoCOG0012', 'MitoCOG0010', 'MitoCOG0004', 'MitoCOG0005', 'MitoCOG0011', 'MitoCOG0039', 'MitoCOG0060', 'MitoCOG0071', 'MitoCOG0059', 'MitoCOG0067', 'MitoCOG0066']
+COG25_gene_list         = ['223163', '223176', '223175', '223607', '223159', '223165', '223170', '223164', '223158', '223172', '223128', '223665', '223275', '223328', '223280', '223127', '223279', '273102', '223130', '223181', '223180', '223168', '223178', '223596', '223556']
+
+
+setname2genes = dict()
+setname2genes['M24']   = M24_gene_list
+setname2genes['COG25'] = COG25_gene_list
+
+
+gene2num = {}
+gene2dl = {}
+for gene_id in (M24_gene_list + COG25_gene_list):
+    pwd_tree_file  = '%s/%s.treefile' % (tree_dir, gene_id)
+    pwd_iqtree_log = '%s/%s.iqtree'   % (tree_dir, gene_id)
+    rows = open(pwd_iqtree_log).read().strip().split("\n")
+    idx = [idx for idx, v in enumerate(rows) if "deltaL  bp-RELL" in v][0]
+    r1, r2 = rows[idx + 2], rows[idx + 3]
+    r1 = [_ for _ in r1.strip().split(" ") if _]
+    r2 = [_ for _ in r2.strip().split(" ") if _]
+    if r2[2] == "0":
+        gene2dl[gene_id] = float(r1[2])
+    else:
+        gene2dl[gene_id] = float(r2[2])
+    gene2num[gene_id] = len(Tree(pwd_tree_file).get_leaf_names())
+
+# plot 1
+for setname, genes in setname2genes.items():
+    dl_list = [gene2dl[_] for _ in genes]
+    dl_list = sorted(dl_list, reverse=True)
+    fig = go.Figure()
+    fig.add_bar(y=dl_list)
+    fig.update_layout(title_text=setname,title_x=0.5,title_y=1,width=700,height=100,template='simple_white',
+                     margin_b=10,margin_l=10,margin_r=10,margin_t=10)
+    fig.write_image('%s/Plot_1_%s.pdf' % (plot_dir, setname))
+
+for gene_set in gene_names:
+    for _model in ['LG']:  # C60
+        t = []
+        for f in glob(f'{indir}/{gene_set}/r*/1pf_{_model}/mcmctree/mcmc.txt'):
+            if exists(f.replace('mcmc.txt', 'FigTree.tre')):
+                t.append((f.split('/')[-4] + ' MCMC', f))
+        t = sorted(t, key=lambda x: int(x[0].split(' ')[0][1:]))
+
+        dfs = []
+        targets = []
+        for cal, mcmc in tqdm(t):
+            tre = get_node_name_from_log(mcmc.replace('mcmc.txt','03_mcmctree.log'))
+            df  = read_mcmc(mcmc)
+            try:
+                df = df.sample(5000)
+            except:
+                print(mcmc)
+            for lca, name in [('GCA_001828545.1,GCA_005524015.1', 'Anammox'), ('GCA_013697045.1,GCA_002356115.1', 'Gamma-AOB'),
+                              ('GCA_001772005.1,GCA_013521015.1', 'Beta-AOB'), ('GCA_017879665.1,GCA_013140535.1', 'Comammox'),
+                              ('Acanthamoeba_castellanii,Andalucia_godoyi', 'Euk'), ('Andalucia_godoyi,Ostreococcus_tauri', 'Euk'),
+                              ('Cyanophora_paradoxa,NC_002186.1', 'Euk')]:
+                try:
+                    n = tre.get_common_ancestor(lca.split(',')).name
+                    targets.append(str(n))
+                    n = 't_n' + str(n)
+                    times = df[[n]]
+                except:
+                    continue
+
+                times.columns = ['time']
+                times.loc[:, 'group name'] = name
+                times.loc[:, 'cal'] = cal
+                dfs.append(times)
+
+        # plot 2
+        _df = pd.concat(dfs, axis=0)
+        g2color = {"Gamma-AOB": "#78fce0", "Beta-AOB": "#956bb4", "Comammox": "#edc21a", "Anammox": "#ff8000"}
+        _df = _df.loc[_df["group name"].isin(list(g2color)), :]
+        _fig = px.violin( _df, y="cal", x="time", color="group name", color_discrete_map=g2color, points=False, orientation="h")
+        _fig.update_traces(side="positive", fillcolor='rgba(0,0,0,0)', width=1.8)
+        _fig.update_traces(showlegend=False)
+        num_y = len(_df["cal"].unique())
+        _fig.layout.template = "simple_white"
+        _fig.layout.width = 700
+        _fig.layout.height = 750
+        _fig.update_xaxes(range=[40, 0])
+        _fig.update_layout(margin_t=10, title_text=f'{gene_set} {_model}', title_x=0.5)
+        _fig.write_image(f'{plot_dir}/Plot_2_{gene_set}_gradient_{_model}.pdf')
+
+        # plot 3
+        xs = []
+        ys = []
+        for ng, subdf in sorted(_df.groupby('cal'),key=lambda x: int(x[0].split(' ')[0].replace('r', ''))):
+            t1 = subdf.loc[subdf['group name'] == 'Gamma-AOB', 'time'].median()
+            t2 = subdf.loc[subdf['group name'] == 'Anammox', 'time'].median()
+            deltaT = t2-t1
+            ys.append(deltaT)
+            xs.append(int(ng.split(' ')[0].replace('r', '')))
+        fig = go.Figure()
+        fig.add_scatter(x=xs, y=ys, mode='markers+lines', showlegend=False)
+        fig.update_layout(width=300, height=300, margin_t=30, margin_l=10, margin_b=10, margin_r=10,
+                          template='simple_white', title_text=f'{gene_set} {_model}', title_x=0.5)
+        fig.write_image('%s/Plot_3_%s_%s.pdf' % (plot_dir, gene_set, _model))
+

TreeSAK/prep_mcmctree_ctl.py

@@ -0,0 +1,92 @@
+import itertools
+
+
+def prep_mcmctree_ctl(ctl_para_dict, mcmctree_ctl_file):
+
+    with open(mcmctree_ctl_file, 'w') as ctl_file_handle:
+        ctl_file_handle.write('      finetune = %s\n' % ctl_para_dict.get('seed',           '-1'))
+        ctl_file_handle.write('       seqfile = %s\n' % ctl_para_dict['seqfile'])
+        ctl_file_handle.write('      treefile = %s\n' % ctl_para_dict['treefile'])
+        ctl_file_handle.write('      mcmcfile = %s\n' % ctl_para_dict['mcmcfile'])
+        ctl_file_handle.write('       outfile = %s\n' % ctl_para_dict['outfile'])
+        ctl_file_handle.write('         ndata = %s\n' % ctl_para_dict.get('ndata',          1))
+        ctl_file_handle.write('       seqtype = %s\n' % ctl_para_dict['seqtype'])
+        ctl_file_handle.write('       usedata = %s\n' % ctl_para_dict['usedata'])
+        ctl_file_handle.write('         clock = %s\n' % ctl_para_dict['clock'])
+        ctl_file_handle.write('       RootAge = %s\n' % ctl_para_dict.get('RootAge',        '<1.0'))
+        ctl_file_handle.write('         model = %s\n' % ctl_para_dict.get('model',          0))
+        ctl_file_handle.write('         alpha = %s\n' % ctl_para_dict.get('alpha',          0.5))
+        ctl_file_handle.write('         ncatG = %s\n' % ctl_para_dict.get('ncatG',          4))
+        ctl_file_handle.write('     cleandata = %s\n' % ctl_para_dict.get('cleandata',      0))
+        ctl_file_handle.write('       BDparas = %s\n' % ctl_para_dict.get('BDparas',        '1 1 0.1'))
+        ctl_file_handle.write('   kappa_gamma = %s\n' % ctl_para_dict.get('kappa_gamma',    '6 2'))
+        ctl_file_handle.write('   alpha_gamma = %s\n' % ctl_para_dict.get('alpha_gamma',    '1 1'))
+        ctl_file_handle.write('   rgene_gamma = %s\n' % ctl_para_dict.get('rgene_gamma',    '1 50 1'))
+        ctl_file_handle.write('  sigma2_gamma = %s\n' % ctl_para_dict.get('sigma2_gamma',   '1 10 1'))
+        ctl_file_handle.write('      finetune = %s\n' % ctl_para_dict.get('finetune',       '1: .1 .1 .1 .1 .1 .1'))
+        ctl_file_handle.write('         print = %s\n' % ctl_para_dict.get('print',          1))
+        ctl_file_handle.write('        burnin = %s\n' % ctl_para_dict.get('burnin',         50000))
+        ctl_file_handle.write('      sampfreq = %s\n' % ctl_para_dict.get('sampfreq',       5))
+        ctl_file_handle.write('       nsample = %s\n' % ctl_para_dict.get('nsample',        50000))
+
+
+mcmctree_ctl_dict = {'seqfile' : 'concatenated.phy',
+                     'treefile': 'deltall75_pa75_rooted_with_calibrations.nwk',
+                     'mcmcfile': 'mcmc.txt',
+                     'outfile' : 'DateArTree_out.txt',
+                     'seqtype' : 2,
+                     'usedata' : 3,
+                     'clock'   : 3}
+
+
+prep_mcmctree_ctl(mcmctree_ctl_dict, '/Users/songweizhi/Desktop/aaa.txt')
+
+
+def get_parameter_combinations(para_to_test_dict):
+
+    para_lol_name = []
+    para_lol_value = []
+    para_lol_name_with_value = []
+    for each_para in sorted(list(para_to_test_dict.keys())):
+        para_setting_list_name = []
+        para_setting_list_value = []
+        para_setting_list_name_with_value = []
+        for each_setting in sorted(para_to_test_dict[each_para]):
+            name_str = ('%s%s' % (each_para, each_setting)).replace(' ', '_')
+            para_setting_list_name.append(each_para)
+            para_setting_list_value.append(each_setting)
+            para_setting_list_name_with_value.append(name_str)
+        para_lol_name.append(para_setting_list_name)
+        para_lol_value.append(para_setting_list_value)
+        para_lol_name_with_value.append(para_setting_list_name_with_value)
+
+    all_combination_list_name = [p for p in itertools.product(*para_lol_name)]
+    all_combination_list_value = [p for p in itertools.product(*para_lol_value)]
+    all_combination_list_name_with_value = [p for p in itertools.product(*para_lol_name_with_value)]
+    all_combination_list_name_with_value_str = ['_'.join(i) for i in all_combination_list_name_with_value]
+
+    para_dod = dict()
+    element_index = 0
+    for each_combination in all_combination_list_name_with_value_str:
+        current_name_list   = all_combination_list_name[element_index]
+        current_value_list  = all_combination_list_value[element_index]
+        current_para_dict = dict()
+        for key, value in zip(current_name_list, current_value_list):
+            current_para_dict[key] = value
+        para_dod[each_combination] = current_para_dict
+        element_index += 1
+
+    return para_dod
+
+
+para_to_test_dict = {'clock': [2, 3], 'nsample': [20000, 50000], 'model': [0, 4], 'kappa_gamma': ['6 2', '5 1']}
+para_dod = get_parameter_combinations(para_to_test_dict)
+print(para_dod)
+
+# all_combination_list_in_str = ['_'.join(i) for i in all_combination_list]
+# print(all_combination_list_in_str)
+# print(len(all_combination_list_in_str))
+
+
+
+

TreeSAK/print_leaves.py

@@ -0,0 +1,32 @@
+import argparse
+from ete3 import Tree
+
+
+print_leaves_usage = '''
+======= print_leaves example commands =======
+
+TreeSAK print_leaves -i in.tree
+
+=============================================
+'''
+
+
+def print_leaves(args):
+
+    tree_file_in = args['i']
+
+    leaf_list = []
+    for leaf in Tree(tree_file_in, format=1):
+        leaf_name = leaf.name
+        leaf_list.append(leaf_name)
+
+    print('\n'.join(sorted(leaf_list)))
+
+
+if __name__ == '__main__':
+
+    # initialize the options parser
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i',      required=True,   help='input tree file')
+    args = vars(parser.parse_args())
+    print_leaves(args)