treesak 1.53.3__py3-none-any.whl

TreeSAK/VisHPD95.py

@@ -0,0 +1,200 @@
+import os
+import glob
+import argparse
+from ete3 import Tree
+from TreeSAK.TreeSAK_config import config_dict
+
+
+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
+
+
+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/DemoData/VisHPD95
+
+==================================================================================
+'''
+
+
+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/ale_parser.py

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+import sys
+import os
+import argparse
+
+
+def ale_parser(rec_folder, options):
+    rec_files = [x for x in os.listdir(rec_folder) if x.endswith("uml_rec")]
+
+    table_info = list()
+    table_events = list()
+
+    for rec_file in rec_files:
+        with open(os.path.join(rec_folder, rec_file)) as f:
+            fam = rec_file.replace(".ale.uml_rec", "")
+
+            lines = f.readlines()
+            stree = lines[2].strip()
+            ll = lines[6].strip().split()[-1]
+            dp, tp, lp = lines[8].strip().split("\t")[1:]
+            n_reconciled_trees = int(lines[9].strip().split()[0])
+            reconciled_trees = lines[11:n_reconciled_trees + 11]
+            de, te, le, se = lines[11 + n_reconciled_trees + 1].split("\t")[1:]
+            table = lines[11 + n_reconciled_trees + 3:]
+
+        table_info.append((fam, ll, dp, tp, lp, de, te, le, se))
+        table_events.append((fam, table))
+
+    if options[0]:
+        with open("SpeciesTreeRef.newick", "w") as f:
+            f.write(stree.split("\t")[-1])
+
+    if options[1]:
+
+        with open("TableInfo.tsv", "w") as f:
+            head = "\t".join(["Family", "LL", "Dp", "Tp", "Lp", "De", "Te", "Le", "Se"]) + "\n"
+            f.write(head)
+            for info in table_info:
+                f.write("\t".join(info))
+
+    if options[2]:
+
+        with open("TableEvents.tsv", "w") as f:
+
+            header = "Family\tBranchType\t" + table[0].replace("# of", "Branch")
+            f.write(header)
+
+            for fam, events in table_events:
+                for b in events[1:]:
+                    f.write(fam + "\t" + b)
+
+    if options[3]:
+        with open("GeneTrees.nwk", "w") as f:
+            for t in reconciled_trees:
+                f.write(t)
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", help="Folder with uml_rec files")
+    parser.add_argument("-s", help="Prints species tree to a different file", action='store_true', default=False)
+    parser.add_argument("-f", help="Prints info about the family (LogLikelihood, probabilities and total number of events, to a different file", action='store_true', default=False)
+    parser.add_argument("-t", help="Prints reconciliation table to a different file", action='store_true', default=False)
+    parser.add_argument("-g", help="Prints gene trees to a different file", action='store_true', default=False)
+
+    args = parser.parse_args()
+
+    if args.i == None:
+        print("use python ale_parser.py -h to see options")
+        print("you can run this script just with python ale_parser -i FolderWithRecFiles -sft")
+        exit(0)
+
+    ale_parser(args.i, [args.s, args.f, args.t, args.g])
+

TreeSAK/ale_splitter.py

@@ -0,0 +1,63 @@
+import sys
+import os
+import argparse
+
+
+def ale_splitter(rec_file, options):
+    with open(rec_file) as f:
+
+        lines = f.readlines()
+
+        stree = lines[2].strip()
+        ll = lines[6].strip().split()[-1]
+        rates = lines[8].strip().split("\t")[1:]
+
+        n_reconciled_trees = int(lines[9].strip().split()[0])
+        reconciled_trees = lines[11:n_reconciled_trees + 11]
+        n_of_events = lines[11 + n_reconciled_trees + 1].split("\t")[1:]
+        table = lines[11 + n_reconciled_trees + 3:]
+
+    if options[0]:
+        with open(rec_file.replace("uml_rec", "stree"), "w") as f:
+            f.write(stree.split("\t")[-1])
+    if options[1]:
+        with open(rec_file.replace("uml_rec", "info"), "w") as f:
+            f.write("LL:" + "\t" + ll + "\n")
+            f.write("Dp:" + "\t" + rates[0] + "\n")
+            f.write("Tp:" + "\t" + rates[1] + "\n")
+            f.write("Lp:" + "\t" + rates[2] + "\n")
+            f.write("De:" + "\t" + n_of_events[0] + "\n")
+            f.write("Te:" + "\t" + n_of_events[1] + "\n")
+            f.write("Le:" + "\t" + n_of_events[2] + "\n")
+            f.write("Se:" + "\t" + n_of_events[3] + "\n")
+
+    if options[2]:
+        with open(rec_file.replace("uml_rec", "recs"), "w") as f:
+            for t in reconciled_trees:
+                f.write(t)
+    if options[3]:
+        with open(rec_file.replace("uml_rec", "rec_table"), "w") as f:
+            for e in table:
+                f.write(e)
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", help="Uml_rec file")
+    parser.add_argument("-s", help="Prints species tree to a different file", action='store_true', default=False)
+    parser.add_argument("-f",
+                        help="Prints info about the family (LogLikelihood, probabilities and total number of events, to a different file",
+                        action='store_true', default=False)
+    parser.add_argument("-t", help="Prints reconciliation table to a different file", action='store_true',
+                        default=False)
+    parser.add_argument("-r", help="Prints reconciled gene trees to a different file", action='store_true',
+                        default=False)
+    args = parser.parse_args()
+
+    if args.i == None:
+        print("use python ale_splitter.py -h to see options")
+        print("you can run this script just with python ale_splitter -i XXXX.uml_rec")
+        exit(0)
+
+    ale_splitter(args.i, [args.s, args.f, args.t, args.r])