treesak 1.53.3__py3-none-any.whl

TreeSAK/do_rrtc.rb

@@ -0,0 +1,464 @@
+#! /bin/env ruby
+
+
+################################################################################
+
+# updated on 2023-01-11
+#   auto-detect input type (marginal or joint)
+# updated on 2023-01-09
+#   --rtc a folder as an input allowed
+# updated on 2022-11-18
+#   bugs fixed
+# updated on 2022-11-18 for non-independent ASR based on scm
+
+
+################################################################################
+
+require 'find'
+require 'getoptlong'
+require 'csv'
+require 'parallel'
+require 'bio-nwk'
+require 'colorize'
+
+
+################################################################################
+class Dir
+    def self.mkdirs(path)
+        if(!File.directory?(path))
+            if(!mkdirs(File.dirname(path)))
+                return false;
+            end
+            mkdir(path)
+        end
+        return true
+    end
+end
+
+
+################################################################################
+def mkdir_with_force(outdir, is_force=false, is_tolerate=false)
+  if outdir.class != String
+    raise "outdir wrong? Exiting ......"
+  end
+
+  if ! Dir.exists?(outdir)
+    `mkdir -p #{outdir}`
+  else
+    if is_tolerate
+      ;
+    elsif is_force
+      `rm -rf #{outdir}`
+      `mkdir -p #{outdir}`
+    else
+      raise "The outdir #{outdir} has already existed!"
+    end
+  end
+end
+
+
+def read_infiles(indir, suffix='', is_all_subfolder=false)
+  infiles = Array.new
+  if ! is_all_subfolder
+    Dir.foreach(indir) do |b|
+      next if b =~ /^\./
+      if suffix.is_a?(String)
+        if suffix != ''
+          next if b !~ /#{suffix}$/
+        end
+      elsif suffix.is_a?(Array)
+        next unless suffix.any?{|i| b =~ /#{i}$/ }
+      end
+      infiles << File.join(indir, b)
+    end
+  else
+    Find.find(indir) do |path|
+      next if File.directory?(path)
+      next if File.basename(path) =~ /^\./
+      infiles << path if suffix.is_a?(String) ? path =~ /\.#{suffix}$/ : suffix.any?{|i| path =~ /#{i}$/ }
+    end
+  end
+  return(infiles)
+end
+
+
+def getFilesBySuffices(indir, suffices)
+  files = Array.new
+  infiles = read_infiles(indir)
+  infiles.each do |infile|
+    if suffices.include?(File.extname(infile))
+      files << infile
+    end
+  end
+  return(files)
+end
+
+
+def get_file_path(file)
+  path = File.symlink?(file) ? File.readlink(file) : file
+  return(path)
+end
+
+################################################################################
+
+# all credits to Wolfgang Teuber (https://gitlab.com/knugie)
+
+def weighted_rand(weights = {})
+  raise 'Probabilities must sum up to 1' unless weights.values.inject(&:+) == 1.0
+  raise 'Probabilities must not be negative' unless weights.values.all? { |p| p >= 0 }
+  # Do more sanity checks depending on the amount of trust in the software component using this method,
+  # e.g. don't allow duplicates, don't allow non-numeric values, etc.
+
+  # Ignore elements with probability 0
+  weights = weights.reject { |k, v| v == 0.0 }   # e.g. => {"a"=>0.4, "b"=>0.4, "c"=>0.2}
+
+  # Accumulate probabilities and map them to a value
+  u = 0.0
+  ranges = weights.map { |v, p| [u += p, v] }   # e.g. => [[0.4, "a"], [0.8, "b"], [1.0, "c"]]
+
+  # Generate a (pseudo-)random floating point number between 0.0(included) and 1.0(excluded)
+  u = rand   # e.g. => 0.4651073966724186
+
+  # Find the first value that has an accumulated probability greater than the random number u
+  ranges.find { |p, v| p > u }.last   # e.g. => "b"
+end
+
+################################################################################
+
+class Bio::Tree
+  def de_no_for_tips
+    allTips.each do |tip|
+      tip.name = tip.name.split(' ')[1,100].join('_')
+    end
+  end
+end
+
+
+class Subclade
+  attr_accessor :name, :num
+  def initialize(arr)
+    #@name = arr
+    @name = arr[0].is_a?(Array) ? arr.map{|i|i.sort} : arr.sort
+    #@name = arr[0] =~ /,/ ? arr.map{|i|i.split(',').sort} : arr.sort
+    @num = nil
+  end
+end
+
+
+class Symbiont < Subclade
+  attr_accessor :hosts
+  def initialize(arr)
+    @name = arr
+    @hosts = Array.new
+  end
+  def is_co_evolve?(data:, is_strict:)
+    @host2prob = Hash.new
+    @hosts.map{|i| @host2prob[i]=i.prob }
+    selected_host = is_strict ? @hosts.sort_by{|i| i.prob }.reverse[0] : weighted_rand(@host2prob)
+    if data[selected_host.num-1].to_f >= data[@num-1].to_f
+      return(true)
+    else
+      return(false)
+    end
+  end
+  def is_co_evolve2?(data:, is_strict:)
+    @host2prob = Hash.new
+    @hosts.map{|i| @host2prob[i]=i.prob }
+    selected_host = is_strict ? @hosts.sort_by{|i| i.prob }.reverse[0] : weighted_rand(@host2prob)
+    if selected_host.num.zip(@num).all?{|a, b| data[a-1].to_f >= data[b-1].to_f }
+      return(true)
+    else
+      return(false)
+    end
+  end
+end
+
+
+class Host < Subclade
+  attr_accessor :prob
+  def prob
+    @prob
+  end
+  def prob=(prob)
+    @prob = prob.to_f
+  end
+end
+
+
+##############################################
+def get_lca_bootstrap(names, name2node, tree)
+  nodes = names.map{|i| name2node[i] }
+  lca = tree.lowest_common_ancestor(nodes[0], nodes[1])
+  begin
+    return(lca.bootstrap)
+  rescue
+    raise nodes.join("\t")
+  end
+end
+
+
+def read_mcmctree_out(file)
+  is_start = false
+  tree = nil
+  in_fh = File.open(file, 'r')
+  #(((1_t5, 2_t9) 33 , ((3_t21, (4_t22, 5_t18) 36 ) 35 , (6_t3, 7_t6) 37 ) 34 ) 32 , (((((8_t8, 9_t12) 42 , (10_t23, 11_t14) 43 ) 41 , (12_t2, 13_t4) 44 ) 40 , 14_t24) 39 , ((((15_t30, 16_t20) 48 , 17_t13) 47 , (((18_t11, 19_t10) 51 , ((20_t1, 21_t26) 53 , (22_t7, (23_t19, 24_t27) 55 ) 54 ) 52 ) 50 , ((((25_t25, 26_t17) 59 , 27_t15) 58 , 28_t16) 57 , 29_t29) 56 ) 49 ) 46 , 30_t28) 45 ) 38 ) 31 ;
+  in_fh.each_line do |line|
+    line.chomp!
+    if is_start
+      tree = getTreeObjFromNwkString(line)
+      break
+    end
+    is_start = true if line =~ /^Species tree for FigTree/
+  end
+  in_fh.close
+
+  tree.de_no_for_tips
+
+  #get_internal_node_index(tree)
+  return(tree)
+end
+
+
+def get_rtc(file, root_two_children_names)
+  rtc_info = Hash.new
+  in_fh = File.open(file, 'r')
+  in_fh.each_line do |line|
+    line.chomp!
+    next if line =~ /^#|^$/
+    line_arr = line.split("\t")
+
+    symbiont = line_arr[0].gsub('_', '_').split(',')
+    rtc = Symbiont.new(symbiont)
+
+    (1..line_arr.size-1).each do |index|
+      ele = line_arr[index]
+      host = ele.split(':')[0].gsub('_', '_').split(',')
+      prob = ele.split(':')[1]
+
+      host_obj = Host.new(host)
+      host_obj.prob = prob
+      rtc.hosts << host_obj
+    end
+
+    root_obj = Host.new(root_two_children_names)
+
+    curr_total_prob = rtc.hosts.map{|host|host.prob}.reduce(&:+)
+    if curr_total_prob < 1
+      root_obj.prob = 1 - curr_total_prob
+      rtc.hosts << root_obj
+    end
+
+    rtc_info[symbiont] = rtc
+  end
+  in_fh.close
+  return(rtc_info)
+end
+
+
+def get_scm(file, root_two_children_names)
+  scm_info = Hash.new
+  symbionts = nil
+  in_fh = File.open(file, 'r')
+  rtc = nil
+
+  in_fh.each_line do |line|
+    line.chomp!
+    line_arr = line.split("\t")
+    next if line =~ /^#|^$/
+    if $. == 1
+      symbionts = line_arr.map{|i| i.gsub(' ', '_').split(',') }
+      rtc = Symbiont.new(symbionts)
+      next
+    end
+
+    prob = line_arr[-1].to_f
+    hosts = line_arr[0, line_arr.size-1].map{|i|i.split(',')}
+    hosts.map!{|a| a[0] == 'root' ? root_two_children_names : a } #2023-01, in case of >=1 root (fl; Z)
+    host_obj = Host.new(hosts)
+    host_obj.prob = prob
+    rtc.hosts << host_obj
+  end
+
+  root_obj = Host.new([root_two_children_names] * symbionts.size)
+  curr_total_prob = rtc.hosts.map{|host|host.prob}.reduce(&:+)
+  if curr_total_prob < 1
+    root_obj.prob = 1 - curr_total_prob
+    rtc.hosts << root_obj
+  end
+  scm_info[symbionts] = rtc
+
+  in_fh.close
+  return(scm_info)
+end
+
+
+##############################################
+def auto_detect_mj(rtc_files) # identify whether marginal or joint
+  first_file = rtc_files[0]
+  in_fh = File.open(first_file, 'r')
+  first_line = in_fh.readline.chomp
+  if first_line =~ /:[10] (\b | \.\d+)/x
+    type = 'marginal'
+  else
+    type = 'joint'
+  end
+  in_fh.close
+  STDERR.puts "type auto-detected\t" + type.colorize(:yellow)
+  return(type)
+end
+
+
+##############################################
+if __FILE__ == $0
+  indir = nil
+  infile = nil
+  type = nil
+  rtc_files = Array.new
+  scm_file = nil
+  scm_files = Array.new
+  mcmctxt_file = nil
+  is_rtc = true
+  is_renum = true
+  is_strict = false
+
+  rtc_info = Hash.new
+  scm_info = Hash.new
+
+  ##############################################
+  opts = GetoptLong.new(
+    ['--indir', GetoptLong::REQUIRED_ARGUMENT],
+    ['-i', GetoptLong::REQUIRED_ARGUMENT],
+    ['--marginal', GetoptLong::REQUIRED_ARGUMENT],
+    ['--joint', GetoptLong::REQUIRED_ARGUMENT],
+    ['--rtc', '--rrtc', GetoptLong::REQUIRED_ARGUMENT],
+    ['--mcmctxt', GetoptLong::REQUIRED_ARGUMENT],
+    ['--is_rtc', '--is_rrtc', '--rrtc_file', '--rtc_file', GetoptLong::REQUIRED_ARGUMENT],
+    ['--strict', '--is_strict', GetoptLong::NO_ARGUMENT],
+    ['--no_renum', '--no_re_num', GetoptLong::NO_ARGUMENT],
+  )
+
+
+  opts.each do |opt, value|
+    case opt
+      when '--indir'
+        indir = value
+      when '-i'
+        infile = value
+      when '--marginal'
+        rtc_files = File.directory?(value) ? read_infiles(value) : [value]
+        type = 'marginal'
+      when '--joint'
+        rtc_files = File.directory?(value) ? read_infiles(value) : [value]
+        type = 'joint'
+      when /^--r?rtc(file)?$/
+        rtc_files = File.directory?(value) ? read_infiles(value) : [value]
+      when '--mcmctxt'
+        mcmctxt_file = value
+      when '--is_rtc', '--is_rrtc'
+        is_rtc = value =~ /^true|T$/i ? true : false
+      when '--is_strict', '--strict'
+        is_strict = true
+        STDERR.puts "is_strict:\t" + "true".colorize(:yellow)
+      when '--no_renum', '--no_re_num'
+        is_renum = false
+    end
+  end
+
+
+  ##############################################
+  unless indir.nil?
+    infile = File.join(indir, 'out') # file 'out' from the mcmctree output
+    mcmctxt_file = File.join(indir, 'mcmc.txt')
+    if is_output
+      outdir = File.join(File.dirname(mcmctxt_file), '')
+      out_fh = File.open(outfile, 'w')
+    end
+  end
+
+  type = auto_detect_mj(rtc_files) if type.nil? # identify whether marginal or joint
+
+
+  ##############################################
+  tree = read_mcmctree_out(infile) # "out", NOT "mcmc.txt"
+
+  root_two_children_names = tree.children(tree.root).map{|i|tree.tips(i)[0].name}
+
+  case type
+    when 'marginal'
+      #rtc_info = get_rtc(rtc_file, root_two_children_names)
+      rtc_files.each do |rtc_file|
+        rtc_info.merge! get_rtc(rtc_file, root_two_children_names)
+      end
+    when 'joint'
+    rtc_files.each do |scm_file|
+      # note scm_info
+      scm_info.merge! get_scm(scm_file, root_two_children_names)
+    end
+  else
+    raise "rtc_file or scm_file has to be provided! Exiting ......"
+  end
+
+  name2node, node2name = tree.getNameNodeRela
+  rtc_info.delete_if{|names, rtc| not names.all?{|name|name2node.include?(name)}} unless rtc_info.nil?
+  scm_info.delete_if{|names, rtc| not names.flatten.all?{|name|name2node.include?(name)}} unless rtc_info.nil?
+
+  minus = tree.allTips.size - 1
+
+
+  ##############################################
+  rtc_info.each_pair do |names, rtc|
+    begin
+      rtc.num = get_lca_bootstrap(names, name2node, tree) - minus
+      rtc.hosts.map{|obj|obj.num = get_lca_bootstrap(obj.name, name2node, tree) - minus}
+    rescue
+      raise "species #{names} or #{rtc.hosts} not found"
+    end
+  end
+
+  scm_info.each_pair do |names, rtc|
+    begin
+      rtc.num = names.map{|names2|get_lca_bootstrap(names2, name2node, tree) - minus}
+      scm_info[names].num = rtc.num
+      rtc.hosts.each do |obj|
+        obj_nums = Array.new
+        names = obj.name
+        names.each do |names|
+          obj_nums << get_lca_bootstrap(names, name2node, tree) - minus
+        end
+        obj.num = obj_nums
+      end
+    end
+  end
+
+
+  ##############################################
+  headers = CSV.open(mcmctxt_file, &:readline)
+
+  col_data = Array.new
+  CSV.foreach(mcmctxt_file) do |row|
+    data = row[0].split("\t")
+    if is_rtc
+      if not rtc_info.empty?
+        #col_data << row if rtc_info.all?{|rtc_name, rtcs| rtcs.all?{|rtc| rtc.is_co_evolve?(data)} }
+        col_data << row if rtc_info.all?{|rtc_name, rtc| rtc.is_co_evolve?(data:data, is_strict:is_strict) }
+      elsif not scm_info.empty?
+        col_data << row if scm_info.all?{|rtc_name, rtc| rtc.is_co_evolve2?(data:data, is_strict:is_strict) }
+      end
+    else
+      col_data << row
+    end
+  end
+
+  STDERR.puts "# of samples after filtering\t" + col_data.size.to_s.colorize(:red)
+
+  col_data.each_with_index do |row_arr, index| # row_arr: single-element array
+    if is_renum and index > 0
+      posteriors = row_arr[0].split("\t")
+      posteriors[0] = index
+      row_arr = [posteriors.join("\t")]
+    end
+    puts row_arr
+  end
+end
+
+

TreeSAK/fa2phy.py

@@ -0,0 +1,42 @@
+import argparse
+from Bio import AlignIO
+
+
+fa2phy_usage = '''
+======= fa2phy example commands =======
+
+TreeSAK fa2phy -i msa.fa -o msa.phy
+
+=======================================
+'''
+
+
+def fa2phy(args):
+
+    fasta_in  = args['i']
+    phy_out   = args['o']
+
+    alignment = AlignIO.read(fasta_in, 'fasta')
+
+    max_seq_id_len = 0
+    for each_seq in alignment:
+        seq_id_len = len(each_seq.id)
+        if seq_id_len > max_seq_id_len:
+            max_seq_id_len = seq_id_len
+
+    with open(phy_out, 'w') as msa_out_handle:
+        msa_out_handle.write('%s %s\n' % (len(alignment), alignment.get_alignment_length()))
+        for each_seq in alignment:
+            seq_id = each_seq.id
+            seq_id_with_space = '%s%s' % (seq_id, ' ' * (max_seq_id_len + 2 - len(seq_id)))
+            msa_out_handle.write('%s%s\n' % (seq_id_with_space, str(each_seq.seq)))
+
+
+if __name__ == '__main__':
+
+    # initialize the options parser
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i',      required=True,   help='input MSA in fasta format')
+    parser.add_argument('-o',      required=True,   help='output MSA in phylip format')
+    args = vars(parser.parse_args())
+    fa2phy(args)

TreeSAK/filter_rename_ar53.py

@@ -0,0 +1,118 @@
+import os
+import glob
+import argparse
+from Bio import SeqIO
+
+
+filter_rename_ar53_usage = '''
+===================================== filter_rename_ar53 example commands =====================================
+
+TreeSAK filter_rename_ar53 -i seq_dir -x fa -g interested_gnms.txt -m interested_marker.txt -o seq_dir_renamed
+
+===============================================================================================================
+'''
+
+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)
+    f_ext = f_ext[1:]
+
+    return f_name, f_path, f_base, f_ext
+
+
+def get_shared_uniq_elements(list_1, list_2):
+    shared_set = set(list_1).intersection(list_2)
+    list_1_uniq = []
+    for e1 in list_1:
+        if e1 not in shared_set:
+            list_1_uniq.append(e1)
+    list_2_uniq = []
+    for e2 in list_2:
+        if e2 not in shared_set:
+            list_2_uniq.append(e2)
+    return shared_set, list_1_uniq, list_2_uniq
+
+
+def filter_rename_ar53(args):
+
+    marker_seq_dir          = args['i']
+    marker_seq_ext          = args['x']
+    interested_gnm_txt      = args['g']
+    interested_marker_txt   = args['m']
+    op_dir                  = args['o']
+    force_overwrite         = args['f']
+
+    # create output folder
+    if os.path.isdir(op_dir) is True:
+        if force_overwrite is True:
+            os.system('rm -r %s' % op_dir)
+        else:
+            print('%s exist, program exited!' % op_dir)
+            exit()
+    os.mkdir(op_dir)
+
+    interested_marker_set = set()
+    if os.path.isfile(interested_marker_txt) is True:
+        for each_marker in open(interested_marker_txt):
+            interested_marker_set.add(each_marker.strip())
+        if len(interested_marker_set) == 0:
+            print('No marker provided in %s, program exited!' % interested_gnm_txt)
+            exit()
+
+    interested_gnm_set = set()
+    if os.path.isfile(interested_gnm_txt) is True:
+        for each_gnm in open(interested_gnm_txt):
+            interested_gnm_set.add(each_gnm.strip())
+        if len(interested_gnm_set) == 0:
+            print('No genome provided in %s, program exited!' % interested_gnm_txt)
+            exit()
+
+    marker_seq_re   = '%s/*.%s' % (marker_seq_dir, marker_seq_ext)
+    marker_seq_list = [os.path.basename(i) for i in glob.glob(marker_seq_re)]
+    marker_seq_id_list = [('.'.join(i.split('.')[:-1])) for i in marker_seq_list]
+    if len(marker_seq_list) == 0:
+        print('No file found in %s, program exited!' % marker_seq_dir)
+        exit()
+
+    marker_to_process = set()
+    if len(interested_marker_set) == 0:
+        marker_to_process = marker_seq_id_list
+    else:
+        shared_set, marker_seq_uniq, interested_marker_uniq = get_shared_uniq_elements(marker_seq_id_list, interested_marker_set)
+        if len(interested_marker_uniq) > 0:
+            print('Sequences for the following interested markers were not found:')
+            print(','.join(interested_marker_uniq))
+        marker_to_process = shared_set
+
+    for marker_id in marker_to_process:
+        pwd_file_in  = '%s/%s.%s' % (marker_seq_dir, marker_id, marker_seq_ext)
+        pwd_file_out = '%s/%s.%s' % (op_dir, marker_id, marker_seq_ext)
+        pwd_op_file_handle = open(pwd_file_out, 'w')
+        for each_seq in SeqIO.parse(pwd_file_in, 'fasta'):
+            gnm_id = each_seq.id
+            if os.path.isfile(interested_gnm_txt) is False:
+                pwd_op_file_handle.write('>%s_XXX\n' % gnm_id)
+                pwd_op_file_handle.write('%s\n' % str(each_seq.seq))
+            else:
+                if gnm_id in interested_gnm_set:
+                    pwd_op_file_handle.write('>%s_XXX\n' % gnm_id)
+                    pwd_op_file_handle.write('%s\n' % str(each_seq.seq))
+        pwd_op_file_handle.close()
+
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    filter_rename_ar53_parser = argparse.ArgumentParser()
+    filter_rename_ar53_parser.add_argument('-i',   required=True,                          help='sequence folder')
+    filter_rename_ar53_parser.add_argument('-x',   required=True,                          help='file extension')
+    filter_rename_ar53_parser.add_argument('-g',   required=False, default=None,           help='interested genome, no ext, one id per line')
+    filter_rename_ar53_parser.add_argument('-m',   required=False, default=None,           help='interested marker, no ext, one id per line')
+    filter_rename_ar53_parser.add_argument('-o',   required=True,                          help='output folder')
+    filter_rename_ar53_parser.add_argument('-f',   required=False, action="store_true",    help='force overwrite')
+    args = vars(filter_rename_ar53_parser.parse_args())
+    filter_rename_ar53(args)

TreeSAK/format_leaf_name.py

@@ -0,0 +1,70 @@
+import os
+import argparse
+from ete3 import Tree
+
+
+format_leaf_name_usage = '''
+========= FLN (Format Leaf Name) example commands =========
+
+BioSAK FLN -i input.tree -o output.tree -s2u -nsqm -ndqm
+BioSAK FLN -i input.tree -o output.tree -ns -nsqm
+
+===========================================================
+'''
+
+
+def format_leaf_name(args):
+
+    tree_file_in             = args['i']
+    tree_format              = args['fmt']
+    tree_file_out            = args['o']
+    no_space                 = args['ns']
+    space_to_underscore      = args['s2u']
+    no_single_quotation_mark = args['nsqm']
+    no_double_quotation_mark = args['ndqm']
+
+    if os.path.isfile(tree_file_in) is False:
+        print('Tree file not found, program exited!')
+        exit()
+
+    if (no_space is True) and (space_to_underscore is True):
+        print('Two actions (-ns and -s2u) specified to spaces in tree leaves, program exited!')
+        exit()
+
+    t = Tree(tree_file_in, format=tree_format)
+
+    # get rename dict
+    mag_rename_dict = dict()
+    for leaf in t:
+        leaf_name = leaf.name
+        if space_to_underscore is True:
+            leaf_name = leaf_name.replace(' ', '_')
+        if no_space is True:
+            leaf_name = leaf_name.replace(' ', '')
+        if no_single_quotation_mark is True:
+            leaf_name = leaf_name.replace("'", '')
+        if no_double_quotation_mark is True:
+            leaf_name = leaf_name.replace('"', '')
+        mag_rename_dict[leaf.name] = leaf_name
+
+    for leaf in t:
+        leaf_name = leaf.name
+        leaf_name_new = mag_rename_dict[leaf_name]
+        leaf.name = leaf_name_new
+    t.write(format=tree_format, outfile=tree_file_out)
+
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    format_leaf_name_parser = argparse.ArgumentParser()
+    format_leaf_name_parser.add_argument('-i',                  required=True,                          help='input tree')
+    format_leaf_name_parser.add_argument('-fmt',                required=False, default=1,              help='tree format, default: 1')
+    format_leaf_name_parser.add_argument('-o',                  required=True,                          help='output tree')
+    format_leaf_name_parser.add_argument('-s2u',                required=False, action="store_true",    help='change space in tree leaves to underscore')
+    format_leaf_name_parser.add_argument('-ns',                 required=False, action="store_true",    help='remove space from leaf names')
+    format_leaf_name_parser.add_argument('-nsqm',               required=False, action="store_true",    help='remove single quotation marks from leaf names')
+    format_leaf_name_parser.add_argument('-ndqm',               required=False, action="store_true",    help='remove double quotation marks from leaf names')
+    args = vars(format_leaf_name_parser.parse_args())
+    format_leaf_name(args)