PyamilySeq 0.5.2__py3-none-any.whl → 0.6.0__py3-none-any.whl

PyamilySeq/PyamilySeq_Species.py

@@ -1,67 +1,21 @@
 #from line_profiler_pycharm import profile
 
-from collections import OrderedDict,defaultdict
 import copy
 import math
 import sys
-from tempfile import NamedTemporaryFile
 
 
 
 try:
     from .Constants import *
+    from .clusterings import *
     from .utils import *
 except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
     from Constants import *
+    from clusterings import *
     from utils import *
 
 
-def custom_sort_key(k, dict1, dict2):
-    return (len(dict1[k]), len(dict2[k]))
-
-def sort_keys_by_values(dict1, dict2):
-    sorted_keys = sorted(dict1.keys(), key=lambda k: custom_sort_key(k, dict1, dict2), reverse=True)
-    return sorted_keys
-
-def select_longest_gene(sequences):
-    """Select the longest sequence for each genome."""
-    longest_sequences = {}
-    for seq_id, sequence in sequences.items():
-        genome = seq_id.split('|')[0]  # Assuming genome name can be derived from the sequence ID
-        if genome not in longest_sequences or len(sequence) > len(longest_sequences[genome][1]):
-            longest_sequences[genome] = (seq_id, sequence)
-    return longest_sequences
-
-
-def run_mafft_on_sequences(options, sequences, output_file):
-    """Run mafft on the given sequences and write to output file."""
-    # Create a temporary input file for mafft
-    with NamedTemporaryFile('w', delete=False) as temp_input_file:
-        for header, sequence in sequences.items():
-            temp_input_file.write(f">{header}\n{sequence}\n")
-        temp_input_file_path = temp_input_file.name
-
-    # Run mafft
-    try:
-        with open(output_file, 'w') as output_f:
-            if options.verbose == 'True':
-                subprocess.run(
-                    ['mafft', '--auto', temp_input_file_path],
-                    stdout=output_f,
-                    stderr=sys.stderr,
-                    check=True
-                )
-            else:
-                subprocess.run(
-                    ['mafft', '--auto', temp_input_file_path],
-                    stdout=output_f,
-                    stderr=subprocess.DEVNULL,  # Suppress stderr
-                    check=True
-                )
-    finally:
-        os.remove(temp_input_file_path)  # Clean up the temporary file
-
-
 def process_gene_families(options, directory, output_file):
     """Process each gene family file to select the longest sequence per genome and concatenate aligned sequences."""
     concatenated_sequences = {}
@@ -102,8 +56,10 @@ def process_gene_families(options, directory, output_file):
 
 def gene_presence_absence_output(options, genome_dict, pangenome_clusters_First_sorted, pangenome_clusters_First_sequences_sorted):
     print("Outputting gene_presence_absence file")
-    in_name = options.clusters.split('.')[0]
-    gpa_outfile = open(in_name+'_gene_presence_absence.csv','w')
+    output_dir = os.path.abspath(options.output_dir)
+    in_name = options.clusters.split('.')[0].split('/')[-1]
+    gpa_outfile = os.path.join(output_dir, in_name)
+    gpa_outfile = open(gpa_outfile+'_gene_presence_absence.csv','w')
     gpa_outfile.write('"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences","Avg sequences per isolate","Genome Fragment","Order within Fragment","'
                      '"Accessory Fragment","Accessory Order with Fragment","QC","Min group size nuc","Max group size nuc","Avg group size nuc","')
     gpa_outfile.write('","'.join(genome_dict.keys()))
@@ -113,14 +69,17 @@ def gene_presence_absence_output(options, genome_dict, pangenome_clusters_First_
         gpa_outfile.write('"group_'+str(cluster)+'","","'+str(len(pangenome_clusters_First_sorted[cluster]))+'","'+str(len(sequences))+'","'+str(average_sequences_per_genome)+
                          '","","","","","","","","",""')
 
-        full_out = ''
+
         for genome in genome_dict.keys():
+            full_out = ''
             tmp_list = []
             for value in sequences:
                 if value.split('|')[0] == genome:
                     tmp_list.append(value)
             if tmp_list:
                 full_out += ',"'+''.join(tmp_list)+'"'
+            else:
+                full_out = ',""'
             gpa_outfile.write(full_out)
         gpa_outfile.write('\n')
 
@@ -137,31 +96,7 @@ def gene_presence_absence_output(options, genome_dict, pangenome_clusters_First_
     #         edge_list_outfile.write(line + '\n')
 
 
-def wrap_sequence(sequence, width=60):
-    wrapped_sequence = []
-    for i in range(0, len(sequence), width):
-        wrapped_sequence.append(sequence[i:i + width])
-    return "\n".join(wrapped_sequence)
-
-
-def read_fasta(fasta_file):
-    sequences = {}
-    current_sequence = None
-    with open(fasta_file, 'r') as file:
-        for line in file:
-            line = line.strip()
-            if not line:
-                continue
-            if line.startswith('>'):
-                current_sequence = line[1:]
-                sequences[current_sequence] = ''
-            else:
-                sequences[current_sequence] += line
-    return sequences
-
 
-def reorder_dict_by_keys(original_dict, sorted_keys):
-    return {k: original_dict[k] for k in sorted_keys}
 
 def get_cores(options,genome_dict):
     ##Calculate core groups
@@ -172,409 +107,89 @@ def get_cores(options,genome_dict):
     for group in options.core_groups.split(','):
         calculated_floor = math.floor(int(group) / 100 * len(genome_dict))
         if first == False:
-            # Ensure no overlap
-            # if calculated_floor <= prev_top:
-            #     calculated_floor = prev_top - 1
-
             groups[group] = (calculated_floor,prev_top)
         else:
             groups[group] = (calculated_floor, prev_top)
             first = False
         prev_top = calculated_floor
-        first_core_group = 'first_core_' + group
+        first_core_group = 'First_core_' + group
         cores[first_core_group] = []
         if options.reclustered != None:
             extended_core_group = 'extended_core_' + group
             cores[extended_core_group] = []
             combined_core_group = 'combined_core_' + group
             cores[combined_core_group] = []
-            second_core_group = 'second_core_' + group
+            second_core_group = 'Second_core_' + group
             cores[second_core_group] = []
-            only_second_core_group = 'only_second_core_' + group
+            only_second_core_group = 'only_Second_core_' + group
             cores[only_second_core_group] = []
     return cores, groups
 
 #@profile
-def calc_First_only_core(cluster, pep_num, groups, cores):
+def calc_First_only_core(cluster, First_num, groups, cores):
     groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= pep_num <= fir):
+    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= First_num <= fir):
         res = idx
     family_group = list(groups)[res]
-    cores['first_core_'+family_group].append(cluster)
+    cores['First_core_'+family_group].append(cluster)
 
 #@profile
-def calc_single_First_extended_Second_only_core(pep_num, groups, cores, second_num): # Count gene families extended with StORFs
+def calc_single_First_extended_Second_only_core(cluster, First_num, groups, cores, Second_num): # Count gene families extended with StORFs
     groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= pep_num+second_num <= fir):
+    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= First_num+Second_num <= fir):
         res = idx
     family_group = list(groups)[res]
-    cores['extended_core_' + family_group].append(pep_num)
+    cores['extended_core_' + family_group].append(cluster)
 
 
 #@profile
-def calc_multi_First_extended_Second_only_core(pep_num, groups, cores, second_num): # Count seperately those gene families extended with StORF_Reporter but combined >1 PEP
+def calc_multi_First_extended_Second_only_core(cluster, First_num, groups, cores, Second_num): # Count seperately those gene families extended with StORF_Reporter but combined >1 PEP
     groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= pep_num+second_num <= fir):
+    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= First_num+Second_num <= fir):
         res = idx
     family_group = list(groups)[res]
-    cores['combined_core_' + family_group] += 1
+    cores['combined_core_' + family_group].append(cluster)
 
 
 #@profile
-def calc_Second_only_core(groups, cores, second_num):
+def calc_Second_only_core(cluster, Second_num, groups, cores):
     groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= second_num <= fir):
+    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= Second_num <= fir):
         res = idx
     family_group = list(groups)[res]
-    cores['second_core_' + family_group] += 1
+    cores['Second_core_' + family_group].append(cluster)
 
 #@profile
-def calc_only_Second_only_core(groups, cores, second_num): # only count the true storf onlies
+def calc_only_Second_only_core(cluster, Second_num, groups, cores): # only count the true storf onlies
     groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= second_num <= fir):
+    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= Second_num <= fir):
         res = idx
     family_group = list(groups)[res]
-    cores['only_second_core_' + family_group] += 1
-
-
-
-
-
-#@profile
-def combined_clustering_counting(options, pangenome_clusters_First, reps, combined_pangenome_clusters_First_Second_clustered):
-    num_clustered_First = defaultdict(list)
-    pangenome_clusters_Type = copy.deepcopy(pangenome_clusters_First)
-    list_of_reps = list(reps.keys())
-    for cluster, pep_genomes in pangenome_clusters_First.items():
-        rep = list_of_reps[int(cluster)]  # get the rep of the current pep cluster
-        Com_PEP_Genomes = 0
-        Seconds = 0
-        seen_Seconds = []
-        added_Second_genomes = 0
-        try:  # get the cluster from the storf clusters which contains this rep
-            clustered_combined = combined_pangenome_clusters_First_Second_clustered[rep]  # Not true clusters - I put a PEP as key myself
-            seen_clust_Genomes = []
-            num_clustered_First[cluster].append(rep + '_' + str(len(pep_genomes)))
-            for clust in clustered_combined:
-                if options.sequence_tag not in clust:  # Not good enough at the moment
-                    clust_Genome = clust.split('|')[0]
-                    if clust_Genome not in seen_clust_Genomes:
-                        seen_clust_Genomes.append(clust_Genome)
-                        if clust_Genome not in pep_genomes:
-                            Com_PEP_Genomes += 1
-                    num_clustered_First[cluster].append(clust + '_' + str(reps[clust][1]))
-                elif options.sequence_tag in clust:
-                    Seconds += 1
-                    clust_Genome = clust.split('|')[0]
-                    if clust_Genome not in seen_Seconds:
-                        seen_Seconds.append(clust_Genome)
-                    if clust_Genome not in seen_clust_Genomes:
-                        seen_clust_Genomes.append(clust_Genome)
-                        if clust_Genome not in pep_genomes:
-                            added_Second_genomes += 1
-                else:
-                    sys.exit("Error: looking for sequence_tag")
-
-            size_of_pep_clusters = []
-            peps = num_clustered_First[cluster]
-            for pep in peps:
-                pep = pep.rsplit('_', 1)
-                size_of_pep_clusters.append(int(pep[1]))
-            pangenome_clusters_Type[cluster] = [len(num_clustered_First[cluster]), sum(size_of_pep_clusters),
-                                                size_of_pep_clusters, added_Second_genomes, Seconds, len(seen_Seconds)]
-
-        except KeyError:
-            ###Singleton
-            num_pep_genomes = [len(pep_genomes)]
-            pangenome_clusters_Type[cluster] = [1, len(pep_genomes), num_pep_genomes, added_Second_genomes, Seconds,
-                                                len(seen_Seconds)]
-
-    return pangenome_clusters_Type
-
-#@profile
-def single_clustering_counting(options, pangenome_clusters_First, reps):
-    num_clustered_First = defaultdict(list)
-    recorded_First = []
-    pangenome_clusters_Type = copy.deepcopy(pangenome_clusters_First)
-    list_of_reps = list(reps.keys())
-    for cluster, First_genomes in pangenome_clusters_First.items():
-        rep = list_of_reps[int(cluster)]  # get the rep of the current pep cluster
-
-        try:  # get the cluster from the storf clusters which contains this rep
-            num_clustered_First[cluster].append(rep + '_' + str(len(First_genomes)))
-            size_of_First_clusters = []
-            Firsts = num_clustered_First[cluster]
-            for First in Firsts:
-                First = First.rsplit('_', 1)
-                size_of_First_clusters.append(int(First[1]))
-                recorded_First.append(First[0])
-            pangenome_clusters_Type[cluster] = [len(num_clustered_First[cluster]), sum(size_of_First_clusters),
-                                                size_of_First_clusters, 0, 0, 0]
-
-        except KeyError:
-            ###Singleton
-            num_pep_genomes = [len(First_genomes)]
-            pangenome_clusters_Type[cluster] = [1, len(First_genomes), num_pep_genomes, 0, 0, 0]
-
-    return pangenome_clusters_Type
-
-
-
-#@profile
-def combined_clustering_CDHIT(options, genome_dict):
-    unique_genomes = []
-    Second_in = open(options.reclustered, 'r')
-    combined_pangenome_clusters_First = OrderedDict()
-    combined_pangenome_clusters_First_sequences = OrderedDict()
-    combined_pangenome_clusters_Second = OrderedDict()
-    combined_pangenome_clusters_Second_sequences = OrderedDict()
-    combined_pangenome_clusters_First_Second_clustered = OrderedDict()
-
-    not_Second_only_cluster_ids = []
-    already_seen_PEP = []
-    Combined_clusters = OrderedDict()
-    Combined_reps = OrderedDict()
-    first = True
-    for line in Second_in:
-        if line.startswith('>'):
-            if first == False:
-                cluster_size = len(Combined_clusters[cluster_id])
-                Combined_reps.update({rep: cluster_size})
-                for pep in combined_pangenome_clusters_First_sequences[cluster_id]:
-                    if pep != []:
-                        if pep in already_seen_PEP:
-                            continue
-                        else:
-                            already_seen_PEP.append(pep)
-                if len(combined_pangenome_clusters_Second_sequences[cluster_id]) > 0 and len(combined_pangenome_clusters_First_sequences[cluster_id]) > 0:
-                    if len(combined_pangenome_clusters_First_sequences[cluster_id]) > 1:  # If we have clustered >1 PEP family, we need to record 1 as key and all others are val
-                        all_but_first = combined_pangenome_clusters_First_sequences[cluster_id][1:]
-                        storfs_clustered = combined_pangenome_clusters_Second_sequences[cluster_id]
-                        VALUE = all_but_first + storfs_clustered
-                    else:
-                        VALUE = combined_pangenome_clusters_Second_sequences[cluster_id]
-                    KEY = combined_pangenome_clusters_First_sequences[cluster_id][0]
-                    combined_pangenome_clusters_First_Second_clustered.update({KEY: VALUE})
-            cluster_id = line.strip('>')
-            cluster_id = cluster_id.strip('\n')
-            cluster_id = cluster_id.split(' ')[1]
-            Combined_clusters.update({cluster_id: []})
-            combined_pangenome_clusters_First.update({cluster_id: []})
-            combined_pangenome_clusters_First_sequences.update({cluster_id: []})
-            combined_pangenome_clusters_Second.update({cluster_id: []})
-            combined_pangenome_clusters_Second_sequences.update({cluster_id: []})
-
-            first = False
-        else:
-            clustered = line.split('\t')[1]
-            clustered = clustered.split('>')[1]
-            clustered = clustered.split('...')[0]
-            genome = clustered.split('|')[0]
-            genome_dict[genome] += 1
-            if '*' in line:
-                rep = clustered
-                Combined_reps.update({rep: 0})
-            if first == False:
-                Combined_clusters[cluster_id].append(clustered)
-                clustered_genome = clustered.split('|')[0]
-                if options.sequence_tag in line:
-                    if clustered_genome not in combined_pangenome_clusters_Second[cluster_id]:
-                        combined_pangenome_clusters_Second[cluster_id].append(clustered_genome)
-                    combined_pangenome_clusters_Second_sequences[cluster_id].append(clustered)
-                else:
-                    if cluster_id not in not_Second_only_cluster_ids:
-                        not_Second_only_cluster_ids.append(cluster_id)  # Tell us which StORF_Reporter clustered are unmatched to a PEP
-                    if clustered_genome not in combined_pangenome_clusters_First[cluster_id]:
-                        combined_pangenome_clusters_First[cluster_id].append(clustered_genome)
-                    combined_pangenome_clusters_First_sequences[cluster_id].append(clustered)
-
-
-    return combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids, combined_pangenome_clusters_Second, unique_genomes
-
-def combined_clustering_Edge_List(options, genome_dict):
-    if options.cluster_format == 'TSV':
-        separator = '\t'
-    elif options.cluster_format == 'CSV':
-        separator = ','
-    unique_genomes = []
-    cluster_id = 0
-    last_rep = ''
-    Second_in = open(options.reclustered, 'r')
-    combined_pangenome_clusters_First = OrderedDict()
-    combined_pangenome_clusters_First_sequences = OrderedDict()
-    combined_pangenome_clusters_Second = OrderedDict()
-    combined_pangenome_clusters_Second_sequences = OrderedDict()
-    combined_pangenome_clusters_First_Second_clustered = OrderedDict()
-
-    not_Second_only_cluster_ids = []
-    already_seen_PEP = []
-    Combined_clusters = OrderedDict()
-    Combined_reps = OrderedDict()
-    first = True
-    for line in Second_in:
-        rep, child = line.strip().split(separator)
-        child_genome = child.split('|')[0]  # Extracting the genome identifier from the child sequence
-
-        if first == True:
-            Combined_clusters.update({cluster_id: []})
-            combined_pangenome_clusters_First.update({cluster_id: []})
-            combined_pangenome_clusters_First_sequences.update({cluster_id: []})
-            combined_pangenome_clusters_Second.update({cluster_id: []})
-            combined_pangenome_clusters_Second_sequences.update({cluster_id: []})
-            Combined_reps.update({rep: 0})
-            first = False
-
-        if first == False:
-            if rep != last_rep and last_rep != '':
-                cluster_size = len(Combined_clusters[cluster_id])
-                Combined_reps.update({rep: cluster_size})
-                for pep in combined_pangenome_clusters_First_sequences[cluster_id]:
-                    if pep != []:
-                        if pep in already_seen_PEP:
-                            continue
-                        else:
-                            already_seen_PEP.append(pep)
-                if len(combined_pangenome_clusters_Second_sequences[cluster_id]) > 0 and len(combined_pangenome_clusters_First_sequences[cluster_id]) > 0:
-                    if len(combined_pangenome_clusters_First_sequences[cluster_id]) > 1:  # If we have clustered >1 PEP family, we need to record 1 as key and all others are val
-                        all_but_first = combined_pangenome_clusters_First_sequences[cluster_id][1:]
-                        storfs_clustered = combined_pangenome_clusters_Second_sequences[cluster_id]
-                        VALUE = all_but_first + storfs_clustered
-                    else:
-                        VALUE = combined_pangenome_clusters_Second_sequences[cluster_id]
-                    KEY = combined_pangenome_clusters_First_sequences[cluster_id][0]
-                    combined_pangenome_clusters_First_Second_clustered.update({KEY: VALUE})
-
-                cluster_id += 1
-                Combined_clusters.update({cluster_id: []})
-                combined_pangenome_clusters_First.update({cluster_id: []})
-                combined_pangenome_clusters_First_sequences.update({cluster_id: []})
-                combined_pangenome_clusters_Second.update({cluster_id: []})
-                combined_pangenome_clusters_Second_sequences.update({cluster_id: []})
-                Combined_reps.update({rep: 0})
-
-
-        Combined_clusters[cluster_id].append(child)
-        if options.sequence_tag in line:
-            if child_genome not in combined_pangenome_clusters_Second[cluster_id]:
-                combined_pangenome_clusters_Second[cluster_id].append(child_genome)
-            combined_pangenome_clusters_Second_sequences[cluster_id].append(child)
-        else:
-            if cluster_id not in not_Second_only_cluster_ids:
-                not_Second_only_cluster_ids.append(cluster_id)  # Tell us which StORF_Reporter clustered are unmatched to a PEP
-            if child_genome not in combined_pangenome_clusters_First[cluster_id]:
-                combined_pangenome_clusters_First[cluster_id].append(child_genome)
-            combined_pangenome_clusters_First_sequences[cluster_id].append(child)
-
-        last_rep = rep
-
-    return combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids, combined_pangenome_clusters_Second, unique_genomes
-
-
-def cluster_EdgeList(options):
-    if options.cluster_format == 'TSV':
-        separator = '\t'
-    elif options.cluster_format == 'CSV':
-        separator = ','
-    cluster_id = 0
-    last_rep = ''
-    first = True
-    First_in = open(options.clusters, 'r')
-    pangenome_clusters_First = OrderedDict()
-    pangenome_clusters_First_sequences = OrderedDict()
-    genome_dict = defaultdict(int)
-    reps = OrderedDict()
-    for line in First_in:
-        rep, child = line.strip().split(separator)
-        child_genome = child.split('|')[0]  # Extracting the genome identifier from the child sequence
-        # Counting occurrences of genomes
-        genome_dict[child_genome] += 1
-        if first == True:
-            pangenome_clusters_First[0] = []
-            pangenome_clusters_First_sequences[0] = []
-            first = False
-
-        if rep != last_rep and last_rep != '':
-            cluster_id +=1
-            pangenome_clusters_First[cluster_id] = []
-            pangenome_clusters_First_sequences[cluster_id] = []
-            cluster_size = len(pangenome_clusters_First_sequences[cluster_id-1])
-            reps.update({last_rep: [cluster_size, len(pangenome_clusters_First[cluster_id-1])]})
-            pangenome_clusters_First[cluster_id] = []
-            pangenome_clusters_First_sequences[cluster_id] = []
-        if child_genome not in pangenome_clusters_First[cluster_id]:
-            pangenome_clusters_First[cluster_id].append(child_genome)
-
-        pangenome_clusters_First_sequences[cluster_id].append(child)
-        last_rep = rep
-        cluster_size = len(pangenome_clusters_First_sequences[cluster_id])
-        reps.update({rep: [cluster_size, len(pangenome_clusters_First[cluster_id])]})
-
-
-    return genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps
+    cores['only_Second_core_' + family_group].append(cluster)
 
 
 
-def cluster_CDHIT(options):
-    First_in = open(options.clusters, 'r')
-    clusters = OrderedDict()
-    pangenome_clusters_First = OrderedDict()
-    pangenome_clusters_First_sequences = OrderedDict()
-    first = True
-    genome_dict = defaultdict(int)
-    reps = OrderedDict()
-    ## Load in all data for easier reuse later
-    for line in First_in:
-        if line.startswith('>'):
-            if first == False:
-                cluster_size = len(clusters[cluster_id])
-                reps.update({rep: [cluster_size, len(pangenome_clusters_First[cluster_id])]})
-            cluster_id = line.strip('>')
-            cluster_id = cluster_id.strip('\n')
-            cluster_id = cluster_id.split(' ')[1]
-            clusters.update({cluster_id: []})
-            pangenome_clusters_First.update({cluster_id: []})
-            pangenome_clusters_First_sequences.update({cluster_id: []})
-
-            first = False
-        else:
-            clustered = line.split('\t')[1]
-            clustered = clustered.split('>')[1]
-            clustered = clustered.split('...')[0]
-            genome = clustered.split('|')[0]
-            genome_dict[genome] += 1
-            if '*' in line:
-                rep = clustered
-                reps.update({rep: [0, 0]})
-            if first == False:
-                clusters[cluster_id].append(clustered)
-                clustered_genome = clustered.split('|')[0]
-                if clustered_genome not in pangenome_clusters_First[cluster_id]:
-                    pangenome_clusters_First[cluster_id].append(clustered_genome)
-                pangenome_clusters_First_sequences[cluster_id].append(clustered)
-    return genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps
-
 #@profile
 def cluster(options):
 
     if options.cluster_format == 'CD-HIT':
-        genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps = cluster_CDHIT(options)
+        genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps = cluster_CDHIT(options, '|')
     elif options.cluster_format in ['TSV','CSV']:
-        genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps = cluster_EdgeList(options)
+        genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps = cluster_EdgeList(options, '|')
 
-    ######################################
+    ###
     cores, groups = get_cores(options, genome_dict)
     ###
 
     if options.reclustered != None:
         if options.cluster_format == 'CD-HIT':
-            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second,\
-                unique_genomes = combined_clustering_CDHIT(options, genome_dict)
-        if options.cluster_format == 'TSV':
-            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second,\
-                unique_genomes = combined_clustering_Edge_List(options, genome_dict)
-        pangenome_clusters_Type = combined_clustering_counting(options, pangenome_clusters_First, reps, combined_pangenome_clusters_First_Second_clustered)
+            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second = combined_clustering_CDHIT(options, genome_dict, '|')
+        if options.cluster_format == ['TSV','CSV']:
+            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second = combined_clustering_Edge_List(options, '|')
+
+        pangenome_clusters_Type = combined_clustering_counting(options, pangenome_clusters_First, reps, combined_pangenome_clusters_First_Second_clustered, '|')
     else:
-        pangenome_clusters_Type = single_clustering_counting(options, pangenome_clusters_First, reps)
+        pangenome_clusters_Type = single_clustering_counting(pangenome_clusters_First, reps)
 
 
 
@@ -588,21 +203,17 @@ def cluster(options):
     print("Calculating Groups")
     for cluster, numbers in pangenome_clusters_Type_sorted.items():
     ############################### Calculate First only
-        #if numbers[0] == 1 and numbers[1] >=2:
         calc_First_only_core(cluster, numbers[1],groups,cores)
 
-        # elif numbers[0] >1 and numbers[1] >=2:
-        #     calc_First_only_core(cluster, numbers[2][0],groups,cores)
-
-
     if options.reclustered != None:
         ############################# Calculate First and Reclustered-Second
         if numbers[0] == 1 and numbers[3] >= 1:  # If Seconds did not combine First reps
-            calc_single_First_extended_Second_only_core(numbers[1], groups, cores, numbers[3])
+            calc_single_First_extended_Second_only_core(cluster, numbers[1], groups, cores, numbers[3])
         elif numbers[0] > 1 and numbers[3] >= 1:  # If unique Secondss combined multiple Firsts
-            calc_multi_First_extended_Second_only_core(numbers[1], groups, cores, numbers[3])
+            calc_multi_First_extended_Second_only_core(cluster, numbers[1], groups, cores, numbers[3])
         elif numbers[4] >= 1:
             Number_Of_Second_Extending_But_Same_Genomes += 1
+
         combined_pangenome_clusters_ONLY_Second_Type = defaultdict(list)
         combined_pangenome_clusters_Second_Type = defaultdict(list)
         for cluster, genomes in combined_pangenome_clusters_Second.items():
@@ -611,26 +222,34 @@ def cluster(options):
             else:
                 combined_pangenome_clusters_ONLY_Second_Type[cluster] = [cluster, len(genomes)]
         for cluster, data in combined_pangenome_clusters_Second_Type.items():
-            calc_Second_only_core(groups, cores, data[1])
+            if data[1] >= 1:
+                calc_Second_only_core(cluster, data[1], groups, cores)
         for cluster, data in combined_pangenome_clusters_ONLY_Second_Type.items():
-            if data[1] >= 2:
-                calc_only_Second_only_core(groups, cores, data[1])
+            if data[1] >= 1:
+                calc_only_Second_only_core(cluster, data[1], groups, cores)
     ###########################
-    key_order = ['first_core_', 'extended_core_', 'combined_core_', 'second_core_','only_second_core_']
-    print("Gene Groups:")
-    for key_prefix in key_order:
-        for key, value in cores.items():
-            if key.startswith(key_prefix):
-                print(f"{key}: {len(value)}")
-    print("Total Number of Gene Groups (Including Singletons): " + str(len(pangenome_clusters_First_sequences_sorted)))
+    ### Output
+    output_path = os.path.abspath(options.output_dir)
+    stats_out = os.path.join(output_path,'summary_statistics.txt')
+    key_order = ['First_core_', 'extended_core_', 'combined_core_', 'Second_core_','only_Second_core_']
+    with open(stats_out, 'w') as outfile:
+        print("Gene Groups:")
+        outfile.write("Gene Groups:\n")
+        for key_prefix in key_order:
+            for key, value in cores.items():
+                if key.startswith(key_prefix):
+                    print(f"{key}: {len(value)}")
+                    outfile.write(f"{key}: {len(value)}\n")
+        print("Total Number of Gene Groups (Including Singletons): " + str(len(pangenome_clusters_First_sequences_sorted)))
+        outfile.write("Total Number of Gene Groups (Including Singletons): " + str(len(pangenome_clusters_First_sequences_sorted)))
 
     if options.gene_presence_absence_out != None:
         gene_presence_absence_output(options,genome_dict, pangenome_clusters_First_sorted, pangenome_clusters_First_sequences_sorted)
 
     if options.write_families != None and options.fasta != None:
         sequences = read_fasta(options.fasta)
-        input_dir = os.path.dirname(os.path.abspath(options.clusters))
-        output_dir = os.path.join(input_dir, 'Gene_Families_Output')
+        output_dir = os.path.dirname(os.path.abspath(options.output_dir))
+        output_dir = os.path.join(output_dir, 'Gene_Families_Output')
 
         # Create output directory if it doesn't exist
         if not os.path.exists(output_dir):
@@ -651,79 +270,9 @@ def cluster(options):
                                         outfile.write(f"{wrapped_sequence}\n")
 
     if options.con_core != None and options.fasta != None and options.write_families != None:
-        process_gene_families(options, os.path.join(input_dir, 'Gene_Families_Output'), 'concatonated_genes_aligned.fasta')
-
-
-        # groups_dir = os.path.join(input_dir, 'Gene_Families_Output')
-        # """Run mafft on all .fasta files in the given directory."""
-        # for filename in os.listdir(groups_dir):
-        #     if filename.endswith('.fasta'):
-        #         input_path = os.path.join(groups_dir, filename)
-        #         output_filename = filename.replace('.fasta', '_mafft.aln')
-        #         output_path = os.path.join(groups_dir, output_filename)
-        #
-        #         # Call mafft command
-        #         try:
-        #             with open(output_path, 'w') as output_file:
-        #                 subprocess.run(
-        #                     ['mafft', '--auto', input_path],
-        #                     stdout=output_file,
-        #                     stderr=subprocess.DEVNULL,  # Suppress stderr
-        #                     check=True
-        #                 )
-        #             print(f"Processed {input_path} -> {output_path}")
-        #         except subprocess.CalledProcessError as e:
-        #             print(f"Failed to process {input_path}: {e}")
-
-        ##This could be run once and not above AND here..
-        # output_dir = os.path.dirname(os.path.abspath(options.clusters))
-        # sequences = read_fasta(options.fasta)
-        # concatenated_sequences = {genome: '' for genome in genome_dict.keys()}
-        #
-        #
-        # for key_prefix in key_order:
-        #     for key, values in cores.items():
-        #         if any(part in options.con_core.split(',') for part in key.split('_')):
-        #             if key.startswith(key_prefix):
-        #                 for value in values:
-        #                     length_capture = {genome: [] for genome in genome_dict.keys()}
-        #                     sequences_to_write = pangenome_clusters_First_sequences_sorted[value]
-        #                     for header in sequences_to_write:
-        #                         if header in sequences:
-        #                             length_capture[header.split('|')[0]].append([header,len(sequences[header])])
-        #                     if all(bool(values) for values in length_capture.values()): # If a GF is not present in 'ALL' genomes, do not add to concat
-        #                         for genome, lengths in length_capture.items():
-        #                             max_value = float('-inf')
-        #                             max_item = None
-        #                             for length in lengths:
-        #                                 current_value = length[1]
-        #                                 if current_value > max_value:
-        #                                     max_value = current_value
-        #                                     max_item = length[0]
-        #                             concatenated_sequences[genome.split('|')[0]] += sequences[max_item]
-        #
-        #
-        # with open(os.path.join(output_dir, 'core_concat.fasta'), 'w') as outfile:
-        #     for genome, sequence in concatenated_sequences.items():
-        #         outfile.write(f">{genome}\n")
-        #         wrapped_sequence = wrap_sequence(sequence)
-        #         outfile.write(f"{wrapped_sequence}\n")
-
-
-        # for core_gene_family in core_gene_families:
-        #     found_sequences = {genome: False for genome in genomes}
-        #
-        #     for fasta_file in fasta_files:f
-        #         sequences = read_fasta(fasta_file)
-        #         for header, sequence in sequences.items():
-        #             genome = header.split('|')[0]
-        #             if genome in genomes and core_gene_family in header:
-        #                 concatenated_sequences[genome] += sequence
-        #                 found_sequences[genome] = True
-        #
-        #     for genome in genomes:
-        #         if not found_sequences[genome]:
-        #             concatenated_sequences[genome] += '-' * len(next(iter(sequences.values())))
+        process_gene_families(options, os.path.join(output_dir, 'Gene_Families_Output'), 'concatonated_genes_aligned.fasta')
+
+