treesak 1.53.3__py3-none-any.whl

TreeSAK/MarkerSeq2Tree.py

@@ -0,0 +1,299 @@
+import os
+import glob
+import argparse
+from Bio import SeqIO
+from Bio import AlignIO
+from distutils.spawn import find_executable
+
+
+MarkerSeq2Tree_usage = '''
+======================== MarkerSeq2Tree example commands ========================
+
+Dependencies: mafft, trimal, bmge, perl and iqtree2
+
+TreeSAK MarkerSeq2Tree -i best_25 -x fa -o op_dir -t 12 -f -bmge -prune 10,20,30
+
+# Note
+"chi2_prune" is performed if you specify "-prune".
+
+=================================================================================
+'''
+
+
+def sep_path_basename_ext(file_in):
+
+    f_path, file_name = os.path.split(file_in)
+    if f_path == '':
+        f_path = '.'
+    f_base, f_ext = os.path.splitext(file_name)
+
+    return f_path, f_base, f_ext
+
+
+def catfasta2phy(msa_dir, msa_ext, concatenated_msa_phy, partition_file):
+
+    concatenated_msa_fasta = '%s.fasta' % concatenated_msa_phy
+    msa_file_re            = '%s/*.%s'  % (msa_dir, msa_ext)
+    msa_file_list          = [os.path.basename(file_name) for file_name in glob.glob(msa_file_re)]
+    msa_file_list_sorted   = sorted(msa_file_list)
+
+    complete_gnm_set = set()
+    for each_msa_file in msa_file_list:
+        pwd_msa = '%s/%s' % (msa_dir, each_msa_file)
+        for each_seq in SeqIO.parse(pwd_msa, 'fasta'):
+            complete_gnm_set.add(each_seq.id)
+
+    complete_gnm_list_sorted = sorted([i for i in complete_gnm_set])
+
+    # initialize concatenated msa dict
+    gnm_to_seq_dict = {i: '' for i in complete_gnm_list_sorted}
+    msa_len_dict = dict()
+    for each_msa_file in msa_file_list_sorted:
+        gene_id = each_msa_file.split('.' + msa_ext)[0]
+
+        # read in msa
+        current_msa_len = 0
+        current_msa_len_set = set()
+        pwd_current_msa = '%s/%s' % (msa_dir, each_msa_file)
+        current_msa_seq_dict = dict()
+        for each_seq in SeqIO.parse(pwd_current_msa, 'fasta'):
+            complete_gnm_set.add(each_seq.id)
+            current_msa_seq_dict[each_seq.id] = str(each_seq.seq)
+            current_msa_len_set.add(len(each_seq.seq))
+            current_msa_len = len(each_seq.seq)
+
+        if len(current_msa_len_set) != 1:
+            print('Sequences with different length were found in %s, program exited!' % each_msa_file)
+            exit()
+
+        msa_len_dict[gene_id] = current_msa_len
+
+        # add sequence to concatenated msa dict
+        for each_gnm in complete_gnm_list_sorted:
+            msa_seq = current_msa_seq_dict.get(each_gnm, current_msa_len*'-')
+            gnm_to_seq_dict[each_gnm] += msa_seq
+
+    # write out concatenated msa
+    concatenated_msa_handle = open(concatenated_msa_fasta, 'w')
+    for each_gnm in complete_gnm_list_sorted:
+        concatenated_msa_handle.write('>%s\n' % each_gnm)
+        concatenated_msa_handle.write('%s\n' % gnm_to_seq_dict[each_gnm])
+    concatenated_msa_handle.close()
+
+    # write out partition file
+    end_pos = 0
+    partition_file_handle = open(partition_file, 'w')
+    for each_m in msa_file_list_sorted:
+        gene_id = each_m.split('.' + msa_ext)[0]
+        current_m_len = msa_len_dict[gene_id]
+        partition_file_handle.write('%s = %s-%s\n' % (each_m, (end_pos + 1), (end_pos + current_m_len)))
+        end_pos += current_m_len
+    partition_file_handle.close()
+
+    # convert msa in fasta to phy
+    AlignIO.convert(concatenated_msa_fasta, 'fasta', concatenated_msa_phy, 'phylip-relaxed')
+
+
+def get_gap_stats(msa_in_fa, stats_txt):
+
+    gap_pct_dict = dict()
+    for each_seq in SeqIO.parse(msa_in_fa, 'fasta'):
+        seq_id = each_seq.id
+        seq_str = str(each_seq.seq)
+        gap_pct = seq_str.count('-')*100/len(seq_str)
+        gap_pct = float("{0:.2f}".format(gap_pct))
+        gap_pct_dict[seq_id] = gap_pct
+
+    gap_pct_sorted = sorted(gap_pct_dict.items(), key=lambda x:x[1])
+
+    stats_txt_handle = open(stats_txt, 'w')
+    stats_txt_handle.write('Sequence\tGap\n')
+    for each_seq in gap_pct_sorted:
+        stats_txt_handle.write('%s\t%s\n' % (each_seq[0], each_seq[1]))
+    stats_txt_handle.close()
+
+
+def BMGE(msa_in, op_prefix, trim_model, entropy_score_cutoff):
+
+    # define file name
+    msa_out_phylip = '%s.BMGE.phylip' % op_prefix
+    msa_out_fasta  = '%s.BMGE.fasta'  % op_prefix
+    msa_out_nexus  = '%s.BMGE.nexus'  % op_prefix
+    msa_out_html   = '%s.BMGE.html'   % op_prefix
+
+    # specify path to BMGE.jar
+    current_file_path   = '/'.join(os.path.realpath(__file__).split('/')[:-1])
+    pwd_bmge_jar        = '%s/BMGE.jar' % current_file_path
+
+    # run BMGE
+    bmge_cmd = 'java -jar %s -i %s -m %s -t AA -h %s -op %s -of %s -on %s -oh %s' % (pwd_bmge_jar, msa_in, trim_model, entropy_score_cutoff, msa_out_phylip, msa_out_fasta, msa_out_nexus, msa_out_html)
+    print('Running %s' % bmge_cmd)
+    os.system(bmge_cmd)
+
+
+def pruneMSA(msa_in, conserved_cutoffs):
+
+    msa_path, msa_base, msa_ext = sep_path_basename_ext(msa_in)
+
+    current_file_path   = '/'.join(os.path.realpath(__file__).split('/')[:-1])
+    alignment_pruner_pl = '%s/alignment_pruner.pl'  % current_file_path
+    cutoff_list         = conserved_cutoffs.split(',')
+
+    op_file_list = []
+    for each_cutoff in cutoff_list:
+        cutoff_formatted    = str(float(each_cutoff)/100)
+        current_msa_out     = '%s_chi2p%s%s'                            % (msa_path, msa_base, each_cutoff, msa_ext)
+        pwd_current_msa_out = '%s/%s_chi2p%s%s'                         % (msa_path, msa_base, each_cutoff, msa_ext)
+        perl_cmd            = 'perl %s --file %s --chi2_prune f%s > %s' % (alignment_pruner_pl,   msa_in, cutoff_formatted, pwd_current_msa_out)
+        perl_cmd_for_report = 'perl %s --file %s --chi2_prune f%s > %s' % ('alignment_pruner.pl', msa_in, cutoff_formatted, pwd_current_msa_out)
+        op_file_list.append(current_msa_out)
+        print(perl_cmd_for_report)
+        os.system(perl_cmd)
+
+    # report
+    print('Pruned MSA exported to:')
+    print('\n'.join(op_file_list))
+
+    return op_file_list
+
+
+def MarkerSeq2Tree(args):
+
+    marker_seq_dir              = args['i']
+    marker_seq_ext              = args['x']
+    op_dir                      = args['o']
+    num_of_threads              = args['t']
+    run_bmge                    = args['bmge']
+    trim_with_bmge              = args['bmge']
+    bmge_trim_model             = args['bmge_m']
+    bmge_entropy_score_cutoff   = args['bmge_esc']
+    force_overwrite             = args['f']
+    alignment_pruner_cutoffs    = args['prune']
+
+    # specify path to BMGE.jar
+    current_file_path = '/'.join(os.path.realpath(__file__).split('/')[:-1])
+    pwd_bmge_jar      = '%s/BMGE.jar' % current_file_path
+
+    # check dependencies
+    not_detected_programs = []
+    for needed_program in ['mafft-einsi', 'trimal', 'iqtree2']:
+        if find_executable(needed_program) is None:
+            not_detected_programs.append(needed_program)
+    if not_detected_programs != []:
+        print('%s not detected, program exited!' % ', '.join(not_detected_programs))
+        exit()
+
+    # get marker id set
+    marker_seq_re   = '%s/*.%s' % (marker_seq_dir, marker_seq_ext)
+    marker_seq_list = sorted(glob.glob(marker_seq_re))
+
+    # define output dir
+    renamed_marker_seq_dir              = '%s/renamed_markers'                      % op_dir
+    renamed_marker_aln_dir              = '%s/renamed_markers_aln'                  % op_dir
+    if trim_with_bmge is False:
+        cmds_2_trim_txt                 = '%s/cmds_2_trimal.txt'                    % op_dir
+        renamed_marker_aln_dir_trimmed  = '%s/renamed_markers_aln_trimal'           % op_dir
+    else:
+        cmds_2_trim_txt                 = '%s/cmds_2_BMGE.txt'                      % op_dir
+        renamed_marker_aln_dir_trimmed  = '%s/renamed_markers_aln_BMGE'             % op_dir
+    concatenated_phy                    = '%s/concatenated.phy'                     % op_dir
+    concatenated_phy_fasta              = '%s/concatenated.phy.fasta'               % op_dir
+    concatenated_phy_partition          = '%s/concatenated_partition.txt'           % op_dir
+    iqtree_dir                          = '%s/iqtree_wd'                            % op_dir
+    cmds_1_mafft_txt                    = '%s/cmds_1_mafft.txt'                     % op_dir
+    cmds_3_iqtree_txt                   = '%s/cmds_3_iqtree2.txt'                   % op_dir
+    pwd_guide_tree                      = '%s/iqtree_wd/guide_tree.treefile'        % op_dir
+
+    # 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)
+    os.mkdir(renamed_marker_seq_dir)
+    os.mkdir(renamed_marker_aln_dir)
+    os.mkdir(renamed_marker_aln_dir_trimmed)
+
+    # write out best hits and extract sequences
+    for marker_seq_file in marker_seq_list:
+
+        f_path, f_base, f_ext = sep_path_basename_ext(marker_seq_file)
+        pwd_renamed_marker_seq          = '%s/%s.%s'  % (renamed_marker_seq_dir, f_base, marker_seq_ext)
+        pwd_renamed_marker_aln          = '%s/%s.aln' % (renamed_marker_aln_dir, f_base)
+        pwd_renamed_marker_aln_trimmed  = '%s/%s.aln' % (renamed_marker_aln_dir_trimmed, f_base)
+
+        # rename sequences
+        marker_hits_seq_renamed_handle = open(pwd_renamed_marker_seq, 'w')
+        for each_seq in SeqIO.parse(marker_seq_file, 'fasta'):
+            seq_id = each_seq.id
+            seq_gnm = '_'.join(seq_id.split('_')[:-1])
+            marker_hits_seq_renamed_handle.write('>%s\n' % seq_gnm)
+            marker_hits_seq_renamed_handle.write('%s\n' % str(each_seq.seq))
+        marker_hits_seq_renamed_handle.close()
+
+        # align
+        mafft_cmd  = 'mafft-einsi --thread %s --quiet %s > %s'          % (num_of_threads, pwd_renamed_marker_seq, pwd_renamed_marker_aln)
+
+        # trim
+        trim_cmd = 'trimal -in %s -out %s -automated1'                  % (pwd_renamed_marker_aln, pwd_renamed_marker_aln_trimmed)
+        if trim_with_bmge is True:
+            trim_cmd = 'java -jar %s -i %s -m %s -t AA -h %s -of %s'    % (pwd_bmge_jar, pwd_renamed_marker_aln, bmge_trim_model, bmge_entropy_score_cutoff, pwd_renamed_marker_aln_trimmed)
+
+        # write out mafft cmds
+        with open(cmds_1_mafft_txt, 'a') as cmds_1_mafft_txt_handle:
+            cmds_1_mafft_txt_handle.write(mafft_cmd + '\n')
+
+        # write out trimal cmds
+        with open(cmds_2_trim_txt, 'a') as cmds_2_trim_txt_handle:
+            cmds_2_trim_txt_handle.write(trim_cmd + '\n')
+
+        # run cmds
+        os.system(mafft_cmd)
+        os.system(trim_cmd)
+
+    # concatenate alignments
+    catfasta2phy(renamed_marker_aln_dir_trimmed, 'aln', concatenated_phy, concatenated_phy_partition)
+
+    # run iqtree2
+    os.mkdir(iqtree_dir)
+    get_guide_tree_cmd  = 'iqtree2 --seqtype AA -T %s -B 1000 --alrt 1000 --quiet -s %s --prefix %s/guide_tree -m LG '                  % (num_of_threads, concatenated_phy, iqtree_dir, )
+    get_c60_tree_cmd    = 'iqtree2 --seqtype AA -T %s -B 1000 --alrt 1000 --quiet -s %s --prefix %s/concatenated -m LG+C60+G+F -ft %s'  % (num_of_threads, concatenated_phy, iqtree_dir, pwd_guide_tree)
+
+    # write out iqtree2 cmds
+    with open(cmds_3_iqtree_txt, 'a') as cmds_3_iqtree_txt_handle:
+        cmds_3_iqtree_txt_handle.write(get_guide_tree_cmd + '\n')
+        cmds_3_iqtree_txt_handle.write(get_c60_tree_cmd + '\n')
+
+    # run alignment_pruner.pl
+    msa_file_list = [concatenated_phy_fasta]
+    if alignment_pruner_cutoffs is not None:
+        pruner_op_file_list = pruneMSA(concatenated_phy_fasta, alignment_pruner_cutoffs)
+        for each_msa in pruner_op_file_list:
+            msa_file_list.append(each_msa)
+
+    # run cmds
+    # print('Running iqtree')
+    # os.system(get_guide_tree_cmd)
+    # os.system(get_c60_tree_cmd)
+
+    print('You may want to submit the following commands to infer tree')
+    print('To be added...')
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    MarkerSeq2Tree_parser = argparse.ArgumentParser()
+    MarkerSeq2Tree_parser.add_argument('-i',           required=True,                          help='marker seq dir')
+    MarkerSeq2Tree_parser.add_argument('-x',           required=True,                          help='marker seq ext')
+    MarkerSeq2Tree_parser.add_argument('-o',           required=True,                          help='output dir')
+    MarkerSeq2Tree_parser.add_argument('-t',           required=False, type=int, default=1,    help='num of threads')
+    MarkerSeq2Tree_parser.add_argument('-bmge',        required=False, action="store_true",    help='perform BMGE trimming on concatenated MSA')
+    MarkerSeq2Tree_parser.add_argument('-bmge_m',      required=False, default='BLOSUM30',     help='BMGE trim model, default: BLOSUM30')
+    MarkerSeq2Tree_parser.add_argument('-bmge_esc',    required=False, default='0.55',         help='BMGE entropy score cutoff, default: 0.55')
+    MarkerSeq2Tree_parser.add_argument('-prune',       required=False, default=None,           help='conservation cutoffs for alignment_pruner.pl')
+    MarkerSeq2Tree_parser.add_argument('-f',           required=False, action="store_true",    help='force overwrite')
+    args = vars(MarkerSeq2Tree_parser.parse_args())
+    MarkerSeq2Tree(args)

TreeSAK/MarkerSeq2Tree_backup.py

@@ -0,0 +1,259 @@
+import os
+import glob
+import argparse
+from Bio import SeqIO
+from Bio import AlignIO
+from distutils.spawn import find_executable
+
+
+MarkerSeq2Tree_usage = '''
+================= MarkerSeq2Tree example commands =================
+
+Dependencies: mafft, trimal, bmge and iqtree2
+
+TreeSAK MarkerSeq2Tree -i best_25 -x fa -o op_dir -t 12 -f -bmge
+
+===================================================================
+'''
+
+
+def sep_path_basename_ext(file_in):
+
+    # separate path and file name
+    f_path, file_name = os.path.split(file_in)
+    if f_path == '':
+        f_path = '.'
+
+    # separate file basename and extension
+    f_base, f_ext = os.path.splitext(file_name)
+
+    return f_path, f_base, f_ext
+
+
+def catfasta2phy(msa_dir, msa_ext, concatenated_msa_phy, partition_file):
+
+    concatenated_msa_fasta = '%s.fasta' % concatenated_msa_phy
+    msa_file_re            = '%s/*.%s'  % (msa_dir, msa_ext)
+    msa_file_list          = [os.path.basename(file_name) for file_name in glob.glob(msa_file_re)]
+    msa_file_list_sorted   = sorted(msa_file_list)
+
+    complete_gnm_set = set()
+    for each_msa_file in msa_file_list:
+        pwd_msa = '%s/%s' % (msa_dir, each_msa_file)
+        for each_seq in SeqIO.parse(pwd_msa, 'fasta'):
+            complete_gnm_set.add(each_seq.id)
+
+    complete_gnm_list_sorted = sorted([i for i in complete_gnm_set])
+
+    # initialize concatenated msa dict
+    gnm_to_seq_dict = {i: '' for i in complete_gnm_list_sorted}
+    msa_len_dict = dict()
+    for each_msa_file in msa_file_list_sorted:
+        gene_id = each_msa_file.split('.' + msa_ext)[0]
+
+        # read in msa
+        current_msa_len = 0
+        current_msa_len_set = set()
+        pwd_current_msa = '%s/%s' % (msa_dir, each_msa_file)
+        current_msa_seq_dict = dict()
+        for each_seq in SeqIO.parse(pwd_current_msa, 'fasta'):
+            complete_gnm_set.add(each_seq.id)
+            current_msa_seq_dict[each_seq.id] = str(each_seq.seq)
+            current_msa_len_set.add(len(each_seq.seq))
+            current_msa_len = len(each_seq.seq)
+
+        if len(current_msa_len_set) != 1:
+            print('Sequences with different length were found in %s, program exited!' % each_msa_file)
+            exit()
+
+        msa_len_dict[gene_id] = current_msa_len
+
+        # add sequence to concatenated msa dict
+        for each_gnm in complete_gnm_list_sorted:
+            msa_seq = current_msa_seq_dict.get(each_gnm, current_msa_len*'-')
+            gnm_to_seq_dict[each_gnm] += msa_seq
+
+    # write out concatenated msa
+    concatenated_msa_handle = open(concatenated_msa_fasta, 'w')
+    for each_gnm in complete_gnm_list_sorted:
+        concatenated_msa_handle.write('>%s\n' % each_gnm)
+        concatenated_msa_handle.write('%s\n' % gnm_to_seq_dict[each_gnm])
+    concatenated_msa_handle.close()
+
+    # write out partition file
+    end_pos = 0
+    partition_file_handle = open(partition_file, 'w')
+    for each_m in msa_file_list_sorted:
+        gene_id = each_m.split('.' + msa_ext)[0]
+        current_m_len = msa_len_dict[gene_id]
+        partition_file_handle.write('%s = %s-%s\n' % (each_m, (end_pos + 1), (end_pos + current_m_len)))
+        end_pos += current_m_len
+    partition_file_handle.close()
+
+    # convert msa in fasta to phy
+    AlignIO.convert(concatenated_msa_fasta, 'fasta', concatenated_msa_phy, 'phylip-relaxed')
+
+
+def get_gap_stats(msa_in_fa, stats_txt):
+
+    gap_pct_dict = dict()
+    for each_seq in SeqIO.parse(msa_in_fa, 'fasta'):
+        seq_id = each_seq.id
+        seq_str = str(each_seq.seq)
+        gap_pct = seq_str.count('-')*100/len(seq_str)
+        gap_pct = float("{0:.2f}".format(gap_pct))
+        gap_pct_dict[seq_id] = gap_pct
+
+    gap_pct_sorted = sorted(gap_pct_dict.items(), key=lambda x:x[1])
+
+    stats_txt_handle = open(stats_txt, 'w')
+    stats_txt_handle.write('Sequence\tGap\n')
+    for each_seq in gap_pct_sorted:
+        stats_txt_handle.write('%s\t%s\n' % (each_seq[0], each_seq[1]))
+    stats_txt_handle.close()
+
+
+def BMGE(msa_in, op_prefix, trim_model, entropy_score_cutoff):
+
+    # define file name
+    msa_out_phylip = '%s.BMGE.phylip' % op_prefix
+    msa_out_fasta  = '%s.BMGE.fasta'  % op_prefix
+    msa_out_nexus  = '%s.BMGE.nexus'  % op_prefix
+    msa_out_html   = '%s.BMGE.html'   % op_prefix
+
+    # specify path to BMGE.jar
+    current_file_path   = '/'.join(os.path.realpath(__file__).split('/')[:-1])
+    pwd_bmge_jar        = '%s/BMGE.jar' % current_file_path
+
+    # run BMGE
+    bmge_cmd = 'java -jar %s -i %s -m %s -t AA -h %s -op %s -of %s -on %s -oh %s' % (pwd_bmge_jar, msa_in, trim_model, entropy_score_cutoff, msa_out_phylip, msa_out_fasta, msa_out_nexus, msa_out_html)
+    print('Running %s' % bmge_cmd)
+    os.system(bmge_cmd)
+
+
+def MarkerSeq2Tree(args):
+
+    marker_seq_dir              = args['i']
+    marker_seq_ext              = args['x']
+    op_dir                      = args['o']
+    num_of_threads              = args['t']
+    run_bmge                    = args['bmge']
+    bmge_trim_model             = args['bmge_m']
+    bmge_entropy_score_cutoff   = args['bmge_esc']
+    force_overwrite             = args['f']
+
+    # check dependencies
+    not_detected_programs = []
+    for needed_program in ['mafft-einsi', 'trimal', 'iqtree2']:
+        if find_executable(needed_program) is None:
+            not_detected_programs.append(needed_program)
+    if not_detected_programs != []:
+        print('%s not detected, program exited!' % ', '.join(not_detected_programs))
+        exit()
+
+    # get marker id set
+    marker_seq_re   = '%s/*.%s' % (marker_seq_dir, marker_seq_ext)
+    marker_seq_list = sorted(glob.glob(marker_seq_re))
+
+    # define output dir
+    renamed_marker_seq_dir              = '%s/renamed_markers'                      % op_dir
+    renamed_marker_aln_dir              = '%s/renamed_markers_aln'                  % op_dir
+    renamed_marker_aln_dir_trimmed      = '%s/renamed_markers_aln_trimmed'          % op_dir
+    concatenated_phy                    = '%s/concatenated.phy'                     % op_dir
+    concatenated_phy_fasta              = '%s/concatenated.phy.fasta'               % op_dir
+    concatenated_phy_fasta_bmge         = '%s/concatenated.BMGE.fasta'              % op_dir
+    concatenated_phy_partition          = '%s/concatenated_partition.txt'           % op_dir
+    bmge_op_prefix                      = '%s/concatenated'                         % op_dir
+    iqtree_dir                          = '%s/iqtree_wd'                            % op_dir
+    cmds_1_mafft_txt                    = '%s/cmds_1_mafft.txt'                     % op_dir
+    cmds_2_trimal_txt                   = '%s/cmds_2_trimal.txt'                    % op_dir
+    cmds_3_iqtree_txt                   = '%s/cmds_3_iqtree2.txt'                   % op_dir
+    pwd_guide_tree                      = '%s/iqtree_wd/guide_tree.treefile'        % op_dir
+
+    # 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)
+    os.mkdir(renamed_marker_seq_dir)
+    os.mkdir(renamed_marker_aln_dir)
+    os.mkdir(renamed_marker_aln_dir_trimmed)
+
+    # write out best hits and extract sequences
+    for marker_seq_file in marker_seq_list:
+
+        f_path, f_base, f_ext = sep_path_basename_ext(marker_seq_file)
+        pwd_renamed_marker_seq          = '%s/%s.%s'  % (renamed_marker_seq_dir, f_base, marker_seq_ext)
+        pwd_renamed_marker_aln          = '%s/%s.aln' % (renamed_marker_aln_dir, f_base)
+        pwd_renamed_marker_aln_trimmed  = '%s/%s.aln' % (renamed_marker_aln_dir_trimmed, f_base)
+
+        # rename sequences
+        marker_hits_seq_renamed_handle = open(pwd_renamed_marker_seq, 'w')
+        for each_seq in SeqIO.parse(marker_seq_file, 'fasta'):
+            seq_id = each_seq.id
+            seq_gnm = '_'.join(seq_id.split('_')[:-1])
+            marker_hits_seq_renamed_handle.write('>%s\n' % seq_gnm)
+            marker_hits_seq_renamed_handle.write('%s\n' % str(each_seq.seq))
+        marker_hits_seq_renamed_handle.close()
+
+        # align and trim
+        mafft_cmd  = 'mafft-einsi --thread %s --quiet %s > %s' % (num_of_threads, pwd_renamed_marker_seq, pwd_renamed_marker_aln)
+        trimal_cmd = 'trimal -in %s -out %s -automated1'       % (pwd_renamed_marker_aln, pwd_renamed_marker_aln_trimmed)
+
+        # write out mafft cmds
+        with open(cmds_1_mafft_txt, 'a') as cmds_1_mafft_txt_handle:
+            cmds_1_mafft_txt_handle.write(mafft_cmd + '\n')
+
+        # write out trimal cmds
+        with open(cmds_2_trimal_txt, 'a') as cmds_2_trimal_txt_handle:
+            cmds_2_trimal_txt_handle.write(trimal_cmd + '\n')
+
+        # run cmds
+        os.system(mafft_cmd)
+        os.system(trimal_cmd)
+
+    # concatenate alignments
+    catfasta2phy(renamed_marker_aln_dir_trimmed, 'aln', concatenated_phy, concatenated_phy_partition)
+
+    # run BMGE
+    if run_bmge is True:
+        BMGE(concatenated_phy_fasta, bmge_op_prefix, bmge_trim_model, bmge_entropy_score_cutoff)
+
+    msa_to_use = concatenated_phy
+    if run_bmge is True:
+        msa_to_use = concatenated_phy_fasta_bmge
+
+    # run iqtree2
+    os.mkdir(iqtree_dir)
+    get_guide_tree_cmd  = 'iqtree2 --seqtype AA -T %s -B 1000 --alrt 1000 --quiet -s %s --prefix %s/guide_tree -m LG '                  % (num_of_threads, msa_to_use, iqtree_dir, )
+    get_c60_tree_cmd    = 'iqtree2 --seqtype AA -T %s -B 1000 --alrt 1000 --quiet -s %s --prefix %s/concatenated -m LG+C60+G+F -ft %s'  % (num_of_threads, msa_to_use, iqtree_dir, pwd_guide_tree)
+
+    # write out iqtree2 cmds
+    with open(cmds_3_iqtree_txt, 'a') as cmds_3_iqtree_txt_handle:
+        cmds_3_iqtree_txt_handle.write(get_guide_tree_cmd + '\n')
+        cmds_3_iqtree_txt_handle.write(get_c60_tree_cmd + '\n')
+
+    # run cmds
+    print('Running iqtree')
+    os.system(get_guide_tree_cmd)
+    os.system(get_c60_tree_cmd)
+
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i',           required=True,                          help='marker seq dir')
+    parser.add_argument('-x',           required=True,                          help='marker seq ext')
+    parser.add_argument('-o',           required=True,                          help='output dir')
+    parser.add_argument('-t',           required=False, type=int, default=1,    help='num of threads')
+    parser.add_argument('-bmge',        required=False, action="store_true",    help='perform BMGE trimming on concatenated MSA')
+    parser.add_argument('-bmge_m',      required=False, default='BLOSUM30',     help='BMGE trim model, default: BLOSUM30')
+    parser.add_argument('-bmge_esc',    required=False, default='0.55',         help='BMGE entropy score cutoff, default: 0.55')
+    parser.add_argument('-f',           required=False, action="store_true",    help='force overwrite')
+    args = vars(parser.parse_args())
+    MarkerSeq2Tree(args)

TreeSAK/ModifyTopo.py

@@ -0,0 +1,116 @@
+from ete3 import Tree
+from os.path import join, dirname, exists
+
+
+def get_topology_without_alpha(st, two_nodes_1, two_nodes_2):
+
+    _st = st.copy()
+    n_replaced = _st.get_common_ancestor(two_nodes_1)
+
+    if len(n_replaced.get_leaf_names()) == 10:
+        n_p = n_replaced.up
+        n_p_p = n_p.up   # All proteobacteria
+        n_p.remove_child(n_replaced)
+        return _st, n_p_p, n_p
+    else:
+        beta_gamma = _st.get_common_ancestor(two_nodes_2)
+        for _ in n_replaced.children[::]:
+            n_replaced.remove_child(_)
+        n_replaced.add_child(beta_gamma)
+        return _st, all_pro, n_replaced
+
+
+def read_tree(in_tree, format=None):
+
+    if isinstance(in_tree, str) and exists(in_tree):
+        if format=='auto':
+            for f in [0,1,2,3,4,5]:
+                try:
+                    t = Tree(in_tree, format=f)
+                    return t
+                except:
+                    pass
+        else:
+            t = Tree(open(in_tree).read(), format=format)
+    elif isinstance(in_tree, Tree):
+        t = in_tree
+    else:
+        raise IOError('unknown input')
+    return t
+
+
+def erase_name(in_tree_file, format=0):
+
+    t = read_tree(in_tree_file, format=format)
+    for n in t.traverse():
+        if not n.is_leaf():
+            n.name = ''
+    return t
+
+
+def get_mito(dataset):
+
+    euk_tree = Tree(euk_reference_tree, 8)
+    euk_tree.prune(dataset)
+    et = erase_name(euk_tree)
+    return {"Mito": et}
+
+
+########################################################################################################################
+
+topo_in_txt = ''
+
+intree                  = f'./dating/topology/mixture_models/deno100/phy/deno100.final_TP1.newick'
+euk_reference_tree      = '/mnt/home-backup/thliao/AOB/analysis/update_calibrations/mito_dating/phylo/manual_topology/euk.tre'
+euk_list_txt            = '/mnt/home-backup/thliao/AOB/analysis/update_calibrations/mito_dating/euk.list'
+base_odir               = "./dating/topology"
+
+Rickettsiales_lineage   = ['GCA_008189685.1', 'GCA_003015145.1']
+Magneto_lineage         = ["GCA_000014865.1", "GCA_002109495.1"]
+remaining_alpha         = ['GCA_000264455.2', 'GCA_002924445.1']
+Holo                    = "GCA_000469665.2"
+two_nodes_1             = ['GCA_000014865.1', 'GCA_000264455.2']
+two_nodes_2             = ['GCA_018655245.1', 'GCA_002356115.1']
+
+TP_dict                 = {"TP1": "((((Holo,other_alpha),Rick),Mito),Magneto);",
+                           "TP2": "(((Holo,other_alpha),(Rick,Mito)),Magneto);",
+                           "TP3": "((((Holo,Rick),other_alpha),Mito),Magneto);",
+                           "TP4": "((((Mito,Rick),Holo),other_alpha),Magneto);"}
+
+# copy from '/home-user/sswang/project/Mito/results/euk_tree/euk.tre'. The Fig S2A in wang 2021 NC
+# rephrase Porphyra purpurea into Porphyra umbilicalis
+# add Polysphondylium pallidum manually
+
+'''
+
+1. provide a input tree
+2. provide a set of tree skeleton
+3. use two leaves to determine a clade.
+
+'''
+
+########################################################################################################################
+
+
+for tp_name, TP in TP_dict.items():
+
+    print('%s\t%s' % (tp_name, TP))
+
+    # get internal node to tree string dict
+
+    st = Tree(intree, 8)
+    _st, all_pro, n_replaced = get_topology_without_alpha(st.copy(), two_nodes_1, two_nodes_2)
+
+    mito_usage = [_ for _ in open(euk_list_txt).read().split('\n')]
+    m_dict = get_mito(mito_usage)
+
+    nodes_dict = {"Rick"        : st.get_common_ancestor(Rickettsiales_lineage),
+                  "other_alpha" : st.get_common_ancestor(remaining_alpha),
+                  "Magneto"     : st.get_common_ancestor(Magneto_lineage),
+                  "Holo"        : [_ for _ in st.traverse() if _.name == Holo][0],
+                  "Mito"        : m_dict['Mito']}
+
+    for k, n in nodes_dict.items():
+        TP = TP.replace(k, n.write(format=3).strip(';'))
+    n_replaced.add_child(Tree(TP, format=3))
+