treesak 1.53.3__py3-none-any.whl

TreeSAK/LcaToLeaves.py

@@ -0,0 +1,66 @@
+import os
+import argparse
+from ete3 import Tree
+
+
+LcaToLeaves_usage = '''
+==================== LcaToLeaves example commands ====================
+
+BioSAK LcaToLeaves -s species_tree.ale.stree -n 123
+BioSAK LcaToLeaves -s species_tree.ale.stree -n internal_nodes.txt
+
+======================================================================
+'''
+
+
+def lca_to_two_leaves(species_tree_from_ale, internal_node_id):
+
+    # read in ale species tree
+    stree_ale = Tree(species_tree_from_ale, format=1)
+
+    # get all leaves of the internal node
+    internal_node = stree_ale.search_nodes(name=internal_node_id)[0]
+    internal_node_leaf_object = internal_node.get_leaves()
+    internal_node_leaf_set = set()
+    for each_leaf in internal_node_leaf_object:
+        internal_node_leaf_set.add(each_leaf.name)
+
+    # get the two leaves needed
+    targeted_two_leaves = []
+    leaves_found = False
+    for leaf_1 in internal_node_leaf_set:
+        for leaf_2 in internal_node_leaf_set:
+            if leaf_1 != leaf_2:
+                if leaves_found is False:
+                    current_lca_id = stree_ale.get_common_ancestor(leaf_1, leaf_2).name
+                    if current_lca_id == internal_node_id:
+                        targeted_two_leaves.append(leaf_1)
+                        targeted_two_leaves.append(leaf_2)
+                        leaves_found = True
+
+    return targeted_two_leaves[0], targeted_two_leaves[1]
+
+
+def LcaToLeaves(args):
+
+    species_tree_from_ale = args['s']
+    internal_node         = args['n']
+
+    internal_node_set = set()
+    if os.path.isfile(internal_node) is False:
+        internal_node_set.add(internal_node)
+    else:
+        for each_node in open(internal_node):
+            internal_node_set.add(each_node.strip())
+
+    for each_internal_node in internal_node_set:
+        leaf_1, leaf_2 = lca_to_two_leaves(species_tree_from_ale, each_internal_node)
+        print('%s\t%s\t%s' % (each_internal_node, leaf_1, leaf_2))
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-s',   required=True,   help='the .stree file from ALE')
+    parser.add_argument('-n',   required=True,   help='internal node(s)')
+    args = vars(parser.parse_args())
+    LcaToLeaves(args)

TreeSAK/MarkerRef2Tree.py

@@ -0,0 +1,616 @@
+import os
+import glob
+import argparse
+from Bio import SeqIO
+from Bio import AlignIO
+import multiprocessing as mp
+from distutils.spawn import find_executable
+
+
+MarkerRef2Tree_usage = '''
+============================= MarkerRef2Tree example commands =============================
+
+Dependencies: java, blastp, mafft-einsi, trimal, iqtree2
+
+# example commands
+TreeSAK MarkerRef2Tree -i faa_files -x faa -m marker_seq -mx fa -o output_dir -bmge -e 10 -t 6 -c 85
+TreeSAK MarkerRef2Tree -i faa_files -x faa -m marker_seq -mx fa -o output_dir -bmge -e 10 -t 6 -c 75,100
+
+# file extension need to be faa
+
+===========================================================================================
+'''
+
+
+def check_dependencies(program_list):
+
+    # check whether executables exist
+    not_detected_programs = []
+    for needed_program in program_list:
+        if find_executable(needed_program) is None:
+            not_detected_programs.append(needed_program)
+
+    # report
+    if not_detected_programs != []:
+        print('%s not found, program exited!' % ','.join(not_detected_programs))
+        exit()
+
+
+def exe_cmds(cmd_list, num_threads):
+    print('Running %s commands with %s cores' % (len(cmd_list), num_threads))
+    pool = mp.Pool(processes=num_threads)
+    pool.map(os.system, cmd_list)
+    pool.close()
+    pool.join()
+
+
+def sep_path_basename_ext(file_in):
+    file_path, file_name = os.path.split(file_in)
+    if file_path == '':
+        file_path = '.'
+    file_basename, file_extension = os.path.splitext(file_name)
+    return file_path, file_basename, file_extension
+
+
+def catfasta2phy(msa_dir, msa_ext, concatenated_msa_phy, concatenated_msa_fasta, partition_file):
+
+    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 fasta to phy
+    AlignIO.convert(concatenated_msa_fasta, 'fasta', concatenated_msa_phy, 'phylip-relaxed')
+
+
+def select_seq(seq_file, id_file,select_option, output_file, one_line, in_fastq):
+
+    # get provided id list
+    seq_id_list = set()
+    for seq_id in open(id_file):
+        seq_id_list.add(seq_id.strip())
+
+    seq_in_format = 'fasta'
+    if in_fastq is True:
+        seq_in_format = 'fastq'
+
+    # extract sequences
+    output_file_handle = open(output_file, 'w')
+    for seq_record in SeqIO.parse(seq_file, seq_in_format):
+        seq_id = seq_record.id
+        if select_option == 1:
+            if seq_id in seq_id_list:
+
+                if in_fastq is False:
+                    if one_line is False:
+                        SeqIO.write(seq_record, output_file_handle, 'fasta')
+                    else:
+                        SeqIO.write(seq_record, output_file_handle, 'fasta-2line')
+                else:
+                    SeqIO.write(seq_record, output_file_handle, 'fastq')
+
+        if select_option == 0:
+            if seq_id not in seq_id_list:
+
+                if in_fastq is False:
+                    if one_line is False:
+                        SeqIO.write(seq_record, output_file_handle, 'fasta')
+                    else:
+                        SeqIO.write(seq_record, output_file_handle, 'fasta-2line')
+                else:
+                    SeqIO.write(seq_record, output_file_handle, 'fastq')
+    output_file_handle.close()
+
+
+def AssessMarkerPA(trimmed_aln_dir, gnm_set, group_to_gnm_dict, present_pct_cutoff_list, op_dir):
+
+    group_to_gnm_num_dict = dict()
+    gnm_to_group_dict     = dict()
+    for each_g in group_to_gnm_dict:
+        gnm_member_list = group_to_gnm_dict[each_g]
+        group_to_gnm_num_dict[each_g] = len(gnm_member_list)
+        for each_gnm in gnm_member_list:
+            gnm_to_group_dict[each_gnm] = each_g
+    group_id_list_sorted = sorted(list(group_to_gnm_dict.keys()))
+
+    # exit program if group information is missing
+    gnms_without_group_info = set()
+    for gnm in gnm_set:
+        if gnm not in gnm_to_group_dict:
+            gnms_without_group_info.add(gnm)
+
+    if len(gnms_without_group_info) > 0:
+        print('Group information for the following genomes are missing, program exited!')
+        print(','.join(gnms_without_group_info))
+        print('Group information for the above genomes are missing, program exited!')
+        exit()
+
+    # read in provided cutoffs
+    assess_summary_1_txt    = '%s/assess_by_PA.txt'                % op_dir
+    assess_summary_2_txt    = '%s/assess_by_PA_summary.txt'        % op_dir
+    itol_binary_txt         = '%s/assess_by_PA_iTOL_binary.txt'    % op_dir
+
+    trimmed_aln_file_re = '%s/*.aln' % (trimmed_aln_dir)
+    trimmed_aln_file_list = [os.path.basename(file_name) for file_name in glob.glob(trimmed_aln_file_re)]
+
+    assess_summary_1_txt_handle = open(assess_summary_1_txt, 'w')
+    assess_summary_1_txt_handle.write('Marker\t%s\n' % '\t'.join([str(i) for i in group_id_list_sorted]))
+    assess_summary_2_txt_handle = open(assess_summary_2_txt, 'w')
+    assess_summary_2_txt_handle.write('Marker\t%s\n' % '\t'.join([str(i) for i in present_pct_cutoff_list]))
+    cutoff_to_qualified_marker_dict = dict()
+    gnm_to_identified_marker_dict = dict()
+    marker_id_list = []
+    for each_aln in trimmed_aln_file_list:
+
+        marker_id = each_aln.split(('.aln'))[0]
+        marker_id_list.append(marker_id)
+        pwd_aln = '%s/%s' % (trimmed_aln_dir, each_aln)
+
+        current_marker_num_by_group_dict = dict()
+        for each_seq in SeqIO.parse(pwd_aln, 'fasta'):
+            gnm_id = each_seq.id
+
+            # get genome to marker dist
+            if gnm_id not in gnm_to_identified_marker_dict:
+                gnm_to_identified_marker_dict[gnm_id] = {marker_id}
+            else:
+                gnm_to_identified_marker_dict[gnm_id].add(marker_id)
+
+            if gnm_id in gnm_to_group_dict:
+                gnm_group = gnm_to_group_dict[gnm_id]
+                if gnm_group not in current_marker_num_by_group_dict:
+                    current_marker_num_by_group_dict[gnm_group] = 1
+                else:
+                    current_marker_num_by_group_dict[gnm_group] += 1
+            else:
+                print('Not all genomes used to generate the MSA being found in -aa, program exited!')
+                exit()
+
+        # write out assess_summary_1_txt
+        pct_list = []
+        for each_grp in group_id_list_sorted:
+            grp_pct = current_marker_num_by_group_dict.get(each_grp, 0)*100/group_to_gnm_num_dict[each_grp]
+            grp_pct = float("{0:.2f}".format(grp_pct))
+            pct_list.append(grp_pct)
+        assess_summary_1_txt_handle.write('%s\t%s\n' % (marker_id, '\t'.join([str(i) for i in pct_list])))
+
+        # write out assess_summary_2_txt
+        assess_list = []
+        for each_cutoff in present_pct_cutoff_list:
+
+            good_marker = True
+            for each_pct in pct_list:
+                if each_pct < each_cutoff:
+                    good_marker = False
+
+            if each_cutoff not in cutoff_to_qualified_marker_dict:
+                cutoff_to_qualified_marker_dict[each_cutoff] = {marker_id}
+
+            if good_marker is True:
+                assess_list.append('1')
+                cutoff_to_qualified_marker_dict[each_cutoff].add(marker_id)
+            else:
+                assess_list.append('0')
+        assess_summary_2_txt_handle.write('%s\t%s\n' % (marker_id, '\t'.join(assess_list)))
+
+    # write out total in assess_summary_2_txt
+    total_stats_list = [str(len(cutoff_to_qualified_marker_dict[each_c])) for each_c in present_pct_cutoff_list]
+    assess_summary_2_txt_handle.write('Total\t%s\n' % ('\t'.join(total_stats_list)))
+    assess_summary_1_txt_handle.close()
+    assess_summary_2_txt_handle.close()
+
+    # copy alignments of qualified marker to corresponding folders
+    for each_cutoff in cutoff_to_qualified_marker_dict:
+        qualified_marker_set        = cutoff_to_qualified_marker_dict[each_cutoff]
+        pwd_qualified_marker_dir    = '%s/marker_PA%s'        % (op_dir, each_cutoff)
+        pwd_qualified_marker_id_txt = '%s/marker_PA%s_id.txt' % (op_dir, each_cutoff)
+
+        os.system('mkdir %s' % pwd_qualified_marker_dir)
+        for each_marker in qualified_marker_set:
+            pwd_marker_aln = '%s/%s.aln' % (trimmed_aln_dir, each_marker)
+            cp_cmd = 'cp %s %s/' % (pwd_marker_aln, pwd_qualified_marker_dir)
+            os.system(cp_cmd)
+
+        # write out id
+        with open(pwd_qualified_marker_id_txt, 'w') as pwd_qualified_marker_id_txt_handle:
+            pwd_qualified_marker_id_txt_handle.write('%s\n' % '\n'.join(qualified_marker_set))
+
+    # write out iTOL file
+    itol_binary_txt_handle = open(itol_binary_txt, 'w')
+    itol_binary_txt_handle.write('DATASET_BINARY\n\nSEPARATOR TAB\nDATASET_LABEL\tlabel1\nCOLOR\t#85C1E9\n')
+    itol_binary_txt_handle.write('SHOW_LABELS\t1\nLABEL_ROTATION\t45\nLABEL_SHIFT\t5\n')
+    itol_binary_txt_handle.write('FIELD_LABELS\t%s\n' % '\t'.join(sorted(marker_id_list)))
+    itol_binary_txt_handle.write('FIELD_SHAPES\t%s\n' % '\t'.join(['1']*len(marker_id_list)))
+    itol_binary_txt_handle.write('\nDATA\n')
+    for each_g in gnm_to_identified_marker_dict:
+        g_identified_marker_set = gnm_to_identified_marker_dict[each_g]
+
+        pa_list = []
+        for each_m in sorted(marker_id_list):
+            if each_m in g_identified_marker_set:
+                pa_list.append('1')
+            else:
+                pa_list.append('-1')
+        itol_binary_txt_handle.write('%s\t%s\n' % (each_g, '\t'.join(pa_list)))
+    itol_binary_txt_handle.close()
+
+    print('Assessment results exported to:\n%s\n%s' % (assess_summary_1_txt, assess_summary_2_txt))
+
+
+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 MarkerRef2Tree(args):
+
+    faa_file_dir                = args['i']
+    faa_file_ext                = args['x']
+    marker_seq_dir              = args['m']
+    marker_seq_ext              = args['mx']
+    gnm_group_txt               = args['g']
+    op_dir                      = args['o']
+    e_value                     = args['e']
+    num_of_threads              = args['t']
+    force_overwrite             = args['f']
+    pa_cutoff_str               = args['c']
+    minimal_marker_number       = args['mmn']
+    run_psiblast                = args['psiblast']
+    trim_with_bmge              = args['bmge']
+    bmge_trim_model             = args['bmge_m']
+    bmge_entropy_score_cutoff   = args['bmge_esc']
+
+    # check dependencies
+    check_dependencies(['java', 'psiblast', 'blastp', 'mafft-einsi', 'trimal', 'iqtree'])
+
+    # specify path to BMGE.jar
+    current_file_path = '/'.join(os.path.realpath(__file__).split('/')[:-1])
+    pwd_bmge_jar      = '%s/BMGE.jar' % current_file_path
+
+    # get marker id set
+    marker_seq_re   = '%s/*.%s' % (marker_seq_dir, marker_seq_ext)
+    marker_seq_list = [os.path.basename(file_name) for file_name in glob.glob(marker_seq_re)]
+    marker_id_set = set()
+    for each_marker_seq_file in marker_seq_list:
+        _, marker_seq_basename, _ = sep_path_basename_ext(each_marker_seq_file)
+        marker_id_set.add(marker_seq_basename)
+
+    # get gnm id list
+    faa_file_re   = '%s/*.%s' % (faa_file_dir, faa_file_ext)
+    faa_file_list = [os.path.basename(file_name) for file_name in glob.glob(faa_file_re)]
+    gnm_set = set()
+    for each_faa_file in faa_file_list:
+        faa_path, faa_basename, faa_ext = sep_path_basename_ext(each_faa_file)
+        gnm_set.add(faa_basename)
+
+    gnm_id_list_sorted = sorted([i for i in gnm_set])
+
+    #################### check genome grouping files ####################
+
+    group_to_gnm_dict = dict()
+    if gnm_group_txt is None:
+        group_to_gnm_dict['group_1'] = set()
+        for each_gnm in gnm_id_list_sorted:
+            group_to_gnm_dict['group_1'].add(each_gnm)
+    else:
+        if os.path.isfile(gnm_group_txt) is False:
+            print('Specified %s not found, program exited!' % gnm_group_txt)
+            exit()
+        else:
+            for each_gnm in open(gnm_group_txt):
+                each_gnm_split = each_gnm.strip().split('\t')
+                gnm_id = each_gnm_split[0]
+                domain_name = each_gnm_split[1]
+                if gnm_id in gnm_set:
+                    if domain_name not in group_to_gnm_dict:
+                        group_to_gnm_dict[domain_name] = {gnm_id}
+                    else:
+                        group_to_gnm_dict[domain_name].add(gnm_id)
+
+    ############################################## check file/folder name ##############################################
+
+    blastp_cmd_txt                          = '%s/s01_blast_cmds_%s.txt'            % (op_dir, (len(marker_seq_list)*len(faa_file_list)))
+    pwd_combined_protein                    = '%s/combined.faa'                     % op_dir
+    blast_op_dir                            = '%s/s01_blast'                        % op_dir
+    best_hit_id_by_marker_dir               = '%s/s02_marker_id'                    % op_dir
+    best_hit_seq_by_marker_dir              = '%s/s03_marker_seq'                   % op_dir
+    best_hit_seq_by_marker_dir_renamed      = '%s/s04_marker_seq_by_genome_name'    % op_dir
+    best_hit_aln_by_marker_dir              = '%s/s05_marker_aln'                   % op_dir
+    best_hit_aln_by_marker_dir_trimmed      = '%s/s06_marker_aln_trimal'            % op_dir
+    if trim_with_bmge is True:
+        best_hit_aln_by_marker_dir_trimmed  = '%s/s06_marker_aln_BMGE'              % op_dir
+    assess_marker_pa_dir                    = '%s/s07_assess_marker_PA'             % op_dir
+    trimmed_msa_PA_concatenated_dir         = '%s/s08_iqtree_wd'                    % op_dir
+    iqtree_dir                              = '%s/s08_iqtree_wd'                    % op_dir
+    iqtree_cmd_txt                          = '%s/iqtree_cmds.txt'                  % iqtree_dir
+
+    ####################################################################################################################
+
+    # create folder
+    if os.path.isdir(op_dir) is True:
+        if force_overwrite is True:
+            os.system('rm -r %s' % op_dir)
+        else:
+            print('Output folder detected, program exited!')
+            exit()
+
+    os.system('mkdir %s' % op_dir)
+    os.system('mkdir %s' % blast_op_dir)
+
+    # get blastp command
+    blast_cmd_list = []
+    blast_op_to_cmd_dict = dict()
+    blastp_cmd_txt_handle = open(blastp_cmd_txt, 'w')
+    for gnm_id in gnm_id_list_sorted:
+        for each_cog in marker_id_set:
+            pwd_blast_op = '%s/%s_vs_%s_blastp.txt'                                                  % (blast_op_dir, gnm_id, each_cog)
+
+            blast_cmd   = 'blastp -subject %s/%s.%s -evalue %s -outfmt 6 -query %s/%s.%s -out %s' % (marker_seq_dir, each_cog, marker_seq_ext, e_value, faa_file_dir, gnm_id, faa_file_ext, pwd_blast_op)
+            if run_psiblast is True:
+                blast_cmd = 'psiblast -subject %s/%s.%s -evalue %s -outfmt 6 -query %s/%s.%s -out %s' % (marker_seq_dir, each_cog, marker_seq_ext, e_value, faa_file_dir, gnm_id, faa_file_ext, pwd_blast_op)
+
+            blast_op_to_cmd_dict[pwd_blast_op] = blast_cmd
+            blastp_cmd_txt_handle.write(blast_cmd + '\n')
+            blast_cmd_list.append(blast_cmd)
+    blastp_cmd_txt_handle.close()
+
+    # run blastp
+    if force_overwrite is True:
+        exe_cmds(blast_cmd_list, num_of_threads)
+    else:
+        cmds_to_rerun = []
+        num_of_good_ones = 0
+        for each_blast_op in blast_op_to_cmd_dict:
+
+            look_good = False
+            if os.path.isfile(each_blast_op) is True:
+                look_good = True
+                num_of_good_ones += 1
+
+            if look_good is False:
+                cmds_to_rerun.append(blast_op_to_cmd_dict[each_blast_op])
+
+        print('Detected blastp outputs: %s' % num_of_good_ones)
+        exe_cmds(cmds_to_rerun, num_of_threads)
+
+    # get best_hit_dict_by_marker
+    best_hit_to_gnm_dict = dict()
+    best_hit_dict_by_marker = dict()
+    for gnm_id in gnm_id_list_sorted:
+        for each_cog in marker_id_set:
+            current_blastp_op = '%s/%s_vs_%s_blastp.txt' % (blast_op_dir, gnm_id, each_cog)
+            # get best hit
+            if os.path.isfile(current_blastp_op) is True:
+                best_hit_gene = ''
+                best_hit_score = 0
+                for each_line in open(current_blastp_op):
+                    each_line_split = each_line.strip().split('\t')
+                    query_id = each_line_split[0]
+                    bit_score = float(each_line_split[11])
+                    if bit_score > best_hit_score:
+                        best_hit_score = bit_score
+                        best_hit_gene = query_id
+
+                if best_hit_gene != '':
+                    best_hit_to_gnm_dict[best_hit_gene] = gnm_id
+
+                    if each_cog not in best_hit_dict_by_marker:
+                        best_hit_dict_by_marker[each_cog] = [best_hit_gene]
+                    else:
+                        best_hit_dict_by_marker[each_cog].append(best_hit_gene)
+
+    # create dir
+    if os.path.isdir(best_hit_id_by_marker_dir) is False:
+        os.system('mkdir %s' % best_hit_id_by_marker_dir)
+    if os.path.isdir(best_hit_seq_by_marker_dir) is False:
+        os.system('mkdir %s' % best_hit_seq_by_marker_dir)
+    if os.path.isdir(best_hit_seq_by_marker_dir_renamed) is False:
+        os.system('mkdir %s' % best_hit_seq_by_marker_dir_renamed)
+    if os.path.isdir(best_hit_aln_by_marker_dir) is False:
+        os.system('mkdir %s' % best_hit_aln_by_marker_dir)
+    if os.path.isdir(best_hit_aln_by_marker_dir_trimmed) is False:
+        os.system('mkdir %s' % best_hit_aln_by_marker_dir_trimmed)
+
+    os.system('cat %s/*.%s > %s' % (faa_file_dir, faa_file_ext, pwd_combined_protein))
+
+    processing_index = 1
+    for each_marker in best_hit_dict_by_marker:
+        print('Processing (extract sequence, align and trim) marker %s/%s: %s' % (processing_index, len(best_hit_dict_by_marker), each_marker))
+        processing_index += 1
+
+        current_m_hit_list      = best_hit_dict_by_marker[each_marker]
+        marker_hits_txt         = ('%s/%s.txt' % (best_hit_id_by_marker_dir,          each_marker)).replace(':', '')
+        marker_hits_seq         = ('%s/%s.fa'  % (best_hit_seq_by_marker_dir,         each_marker)).replace(':', '')
+        marker_hits_seq_renamed = ('%s/%s.fa'  % (best_hit_seq_by_marker_dir_renamed, each_marker)).replace(':', '')
+        marker_hits_aln         = ('%s/%s.aln' % (best_hit_aln_by_marker_dir,         each_marker)).replace(':', '')
+        marker_hits_aln_trimmed = ('%s/%s.aln' % (best_hit_aln_by_marker_dir_trimmed, each_marker)).replace(':', '')
+
+        with open(marker_hits_txt, 'w') as marker_hits_txt_handle:
+            marker_hits_txt_handle.write('\n'.join(current_m_hit_list))
+
+        # extract sequences
+        select_seq(pwd_combined_protein, marker_hits_txt, 1, marker_hits_seq, True, False)
+
+        # rename sequences
+        marker_hits_seq_renamed_handle = open(marker_hits_seq_renamed, 'w')
+        for each_seq in SeqIO.parse(marker_hits_seq, 'fasta'):
+            seq_id = each_seq.id
+            seq_gnm = best_hit_to_gnm_dict[seq_id]
+            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()
+
+        # run mafft-einsi
+        mafft_cmd = 'mafft-einsi --thread %s --quiet %s  > %s' % (num_of_threads, marker_hits_seq_renamed, marker_hits_aln)
+        os.system(mafft_cmd)
+
+        # trim msa
+        trim_cmd = 'trimal -in %s -out %s -automated1' % (marker_hits_aln, marker_hits_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, marker_hits_aln, bmge_trim_model, bmge_entropy_score_cutoff, marker_hits_aln_trimmed)
+        os.system(trim_cmd)
+
+    ########## Assess marker by PA ##########
+
+    present_pct_cutoff_list = [int(i) for i in pa_cutoff_str.split(',')]
+
+    # create output dir
+    if os.path.isdir(assess_marker_pa_dir) is True:
+        os.system('rm -r %s' % assess_marker_pa_dir)
+    os.system('mkdir %s' % assess_marker_pa_dir)
+
+    AssessMarkerPA(best_hit_aln_by_marker_dir_trimmed, gnm_set, group_to_gnm_dict, present_pct_cutoff_list, assess_marker_pa_dir)
+
+    ########## concatenate marker ##########
+
+    # create output dir
+    if os.path.isdir(trimmed_msa_PA_concatenated_dir) is True:
+        os.system('rm -r %s' % trimmed_msa_PA_concatenated_dir)
+    os.system('mkdir %s' % trimmed_msa_PA_concatenated_dir)
+
+    qualified_cutoff_list = []
+    for each_c in present_pct_cutoff_list:
+        current_cutoff_trimmed_msa_dir = '%s/marker_PA%s' % (assess_marker_pa_dir, each_c)
+        trimmed_msa_re   = '%s/*.aln' % current_cutoff_trimmed_msa_dir
+        trimmed_msa_list = [os.path.basename(file_name) for file_name in glob.glob(trimmed_msa_re)]
+
+        if len(trimmed_msa_list) < minimal_marker_number:
+            print('The number of qualified marker under PA cutoff %s: %s, skipped!' % (each_c, len(trimmed_msa_list)))
+        else:
+            qualified_cutoff_list.append(each_c)
+            pwd_concatenated_marker_phy       = '%s/marker_pa%s.phy'           % (trimmed_msa_PA_concatenated_dir, each_c)
+            pwd_concatenated_marker_fasta     = '%s/marker_pa%s.fasta'         % (trimmed_msa_PA_concatenated_dir, each_c)
+            pwd_concatenated_marker_partition = '%s/marker_pa%s_partition.txt' % (trimmed_msa_PA_concatenated_dir, each_c)
+            catfasta2phy(current_cutoff_trimmed_msa_dir, 'aln', pwd_concatenated_marker_phy, pwd_concatenated_marker_fasta, pwd_concatenated_marker_partition)
+
+    ########## get guide tree and C60+PMSF tree for each set of marker set ##########
+
+    iqtree_cmd_txt_handle = open(iqtree_cmd_txt, 'w')
+    iqtree_cmd_list = []
+    for each_c in qualified_cutoff_list:
+        os.system('mkdir %s/PA%s_guide_tree'    % ((iqtree_dir, each_c)))
+        os.system('mkdir %s/PA%s_PMSF_C60_tree' % ((iqtree_dir, each_c)))
+
+        msa_to_use = 'marker_pa%s.fasta' % each_c
+
+        get_guide_tree_cmd = 'iqtree2 --seqtype AA -B 1000 --alrt 1000 --quiet -T %s -s %s --prefix PA%s_guide_tree/PA%s_guide_tree -m LG'                                                       % (num_of_threads, msa_to_use, each_c, each_c)
+        get_c60_tree_cmd   = 'iqtree2 --seqtype AA -B 1000 --alrt 1000 --quiet -T %s -s %s --prefix PA%s_PMSF_C60_tree/PA%s_PMSF_C60 -m LG+C60+F+G -ft PA%s_guide_tree/PA%s_guide_tree.treefile' % (num_of_threads, msa_to_use, each_c, each_c, each_c, each_c)
+        cmds_in_one_line   = '%s; %s' % (get_guide_tree_cmd, get_c60_tree_cmd)
+        iqtree_cmd_txt_handle.write('%s\n' % cmds_in_one_line)
+        iqtree_cmd_list.append(cmds_in_one_line)
+    iqtree_cmd_txt_handle.close()
+
+    # run iqtree
+    os.chdir(iqtree_dir)
+    for each_cmd in iqtree_cmd_list:
+        print('Running: %s' % each_cmd)
+        os.system(each_cmd)
+
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    # initialize the options parser
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i',               required=True,                              help='faa dir')
+    parser.add_argument('-x',               required=False, default='faa',              help='faa file extension, default: faa')
+    parser.add_argument('-m',               required=True,                              help='marker seq dir, file extension need to be faa')
+    parser.add_argument('-mx',              required=False, default='faa',              help='marker seq file extension, default: faa')
+    parser.add_argument('-g',               required=False, default=None,               help='genome group')
+    parser.add_argument('-c',               required=False, default='85',               help='presence-absence cutoffs, default: 85')
+    parser.add_argument('-o',               required=True,                              help='output dir')
+    parser.add_argument('-e',               required=False, default='1e-30',            help='e-value cutoff, default: 1e-30')
+    parser.add_argument('-t',               required=True,  type=int,                   help='num of threads')
+    parser.add_argument('-mmn',             required=False, default=1, type=int,        help='minimal marker number, default: 1')
+    parser.add_argument('-psiblast',        required=False, action="store_true",        help='run psiblast')
+    parser.add_argument('-bmge',            required=False, action="store_true",        help='trim MSA with BMGE, default is trimal')
+    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())
+    MarkerRef2Tree(args)