PyamilySeq 0.5.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

PyamilySeq/PyamilySeq_Genus.py

@@ -1,127 +1,42 @@
 #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):
-    print("Conducting MAFFT alignment.")
-    """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 = {}
-    output_file = directory.replace('Gene_Families_Output',output_file)
-
-    # Iterate over each gene family file
-    for gene_file in os.listdir(directory):
-        if gene_file.endswith('.fasta'):
-            gene_path = os.path.join(directory, gene_file)
-
-            # Read sequences from the gene family file
-            sequences = read_fasta(gene_path)
-
-            # Select the longest sequence for each genome
-            longest_sequences = select_longest_gene(sequences)
-
-            # Run mafft on the longest sequences
-            aligned_file = f"{gene_file}_aligned.fasta"
-            run_mafft_on_sequences(options, {seq_id: seq for seq_id, seq in longest_sequences.values()}, aligned_file)
-
-            # Read aligned sequences and concatenate them
-            aligned_sequences = read_fasta(aligned_file)
-            for genome, aligned_seq in aligned_sequences.items():
-                genome_name = genome.split('|')[0]
-                if genome_name not in concatenated_sequences:
-                    concatenated_sequences[genome_name] = ""
-                concatenated_sequences[genome_name] += aligned_seq
-
-            # Clean up aligned file
-            os.remove(aligned_file)
-
-    # Write the concatenated sequences to the output file
-    with open(output_file, 'w') as out:
-        for genome, sequence in concatenated_sequences.items():
-            out.write(f">{genome}\n")
-            wrapped_sequence = wrap_sequence(sequence, 60)
-            out.write(f"{wrapped_sequence}\n")
-
-def gene_presence_absence_output(options, genome_dict, pangenome_clusters_First_sorted, pangenome_clusters_First_sequences_sorted):
+def gene_presence_absence_output(options, genus_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()))
+    gpa_outfile.write('","'.join(genus_dict.keys()))
     gpa_outfile.write('"\n')
     for cluster, sequences in pangenome_clusters_First_sequences_sorted.items():
         average_sequences_per_genome = len(sequences) / len(pangenome_clusters_First_sorted[cluster])
         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():
+
+        for genus in genus_dict.keys():
+            full_out = ''
             tmp_list = []
             for value in sequences:
-                if value.split('|')[0] == genome:
+                if value.split('_')[0] == genus:
                     tmp_list.append(value)
             if tmp_list:
                 full_out += ',"'+''.join(tmp_list)+'"'
+            else:
+                full_out = ',""'
             gpa_outfile.write(full_out)
         gpa_outfile.write('\n')
 
@@ -138,448 +53,85 @@ 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  # Skip empty lines
-            if line.startswith('>'):
-                current_sequence = line[1:]  # Remove '>' character
-                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):
+def get_cores(options):
     ##Calculate core groups
     groups = OrderedDict()
     cores = OrderedDict()
-    prev_top = len(genome_dict)
-    first = True
     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_genera_' + group
         cores[first_core_group] = []
         if options.reclustered != None:
-            extended_core_group = 'extended_core_' + group
+            extended_core_group = 'extended_genera_' + group
             cores[extended_core_group] = []
-            combined_core_group = 'combined_core_' + group
+            combined_core_group = 'combined_genera_' + group
             cores[combined_core_group] = []
-            second_core_group = 'second_core_' + group
+            second_core_group = 'Second_genera_' + group
             cores[second_core_group] = []
-            only_second_core_group = 'only_second_core_' + group
+            only_second_core_group = 'only_Second_genera_' + group
             cores[only_second_core_group] = []
     return cores, groups
 
 #@profile
-def calc_First_only_core(cluster, pep_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):
-        res = idx
-    family_group = list(groups)[res]
-    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
-    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):
-        res = idx
-    family_group = list(groups)[res]
-    cores['extended_core_' + family_group].append(pep_num)
-
-
-#@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
-    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):
-        res = idx
-    family_group = list(groups)[res]
-    cores['combined_core_' + family_group] += 1
-
-
+def calc_First_only_core(cluster, First_num,  cores):
+    try:
+        cores['First_genera_' + str(First_num)].append(cluster)
+    except KeyError:
+        cores['First_genera_>'].append(cluster)
 #@profile
-def calc_Second_only_core(groups, cores, second_num):
-    groups_as_list = list(groups.values())
-    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
-
+def calc_single_First_extended_Second_only_core(cluster, First_num, cores, Second_num): # Count gene families extended with StORFs
+    group = First_num + Second_num
+    try:
+        cores['extended_genera_' + str(group)].append(cluster)
+    except KeyError:
+        cores['extended_genera_>'].append(cluster)
 #@profile
-def calc_only_Second_only_core(groups, cores, second_num): # 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):
-        res = idx
-    family_group = list(groups)[res]
-    cores['only_second_core_' + family_group] += 1
-
-
-
-
-
+def calc_multi_First_extended_Second_only_core(cluster, First_num, cores, Second_num): # Count seperately those gene families extended with StORF_Reporter but combined >1 PEP
+    group = First_num + Second_num
+    try:
+        cores['combined_genera_' + str(group)].append(cluster)
+    except KeyError:
+        cores['combined_genera_>'].append(cluster)
 #@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
-
+def calc_Second_only_core(cluster, cores, Second_num):
+    try:
+        cores['Second_genera_' + str(Second_num)].append(cluster)
+    except KeyError:
+        cores['Second_genera_>'].append(cluster)
 #@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
-
+def calc_only_Second_only_core(cluster, cores, Second_num): # only count the true storf onlies
+    try:
+        cores['only_Second_genera_' + str(Second_num)].append(cluster)
+    except:
+        cores['only_Second_genera_>'].append(cluster)
 
 
-#@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
-
-
-
-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)
-    elif options.cluster_format in ['TSV','CSV']:
-        genome_dict, pangenome_clusters_First, pangenome_clusters_First_sequences, reps = cluster_EdgeList(options)
+        genus_dict, pangenome_clusters_First, pangenome_clusters_First_genomes, pangenome_clusters_First_sequences, reps = cluster_CDHIT(options, '_')
+    elif 'TSV' in options.cluster_format or 'CSV' in options.cluster_format:
+        genus_dict, pangenome_clusters_First, pangenome_clusters_First_genomes, pangenome_clusters_First_sequences, reps = cluster_EdgeList(options, '_')
 
-    ######################################
-    cores, groups = get_cores(options, genome_dict)
+    ###
+    cores, groups = get_cores(options)
     ###
 
     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_pangenome_clusters_Second_sequences = combined_clustering_CDHIT(options, genus_dict, '_')
+        elif 'TSV' in options.cluster_format or 'CSV' in options.cluster_format:
+            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second, combined_pangenome_clusters_Second_sequences = combined_clustering_Edge_List(options, '_')
+        pangenome_clusters_Type = combined_clustering_counting(options, pangenome_clusters_First, reps, combined_pangenome_clusters_First_Second_clustered, pangenome_clusters_First_genomes, '_')
     else:
-        pangenome_clusters_Type = single_clustering_counting(options, pangenome_clusters_First, reps)
+        pangenome_clusters_Type = single_clustering_counting(pangenome_clusters_First, reps)
 
 
 
-    Number_Of_StORF_Extending_But_Same_Genomes = 0
+    Number_Of_Second_Extending_But_Same_Genomes = 0
 
     sorted_first_keys = sort_keys_by_values(pangenome_clusters_First, pangenome_clusters_First_sequences)
     pangenome_clusters_First_sorted = reorder_dict_by_keys(pangenome_clusters_First, sorted_first_keys)
@@ -587,23 +139,28 @@ def cluster(options):
     pangenome_clusters_Type_sorted = reorder_dict_by_keys(pangenome_clusters_Type, sorted_first_keys)
 
     print("Calculating Groups")
+    seen_groupings = []
     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)
-
+        cluster = str(cluster)
+        for grouping in numbers[2]: #!!# Could do with a more elegant solution
+            current_cluster = grouping[0].split(':')[0]
+            if current_cluster not in seen_groupings:
+                seen_groupings.append(current_cluster)
+                current_cluster_size = grouping[0].split(':')[1]
+                calc_First_only_core(current_cluster, current_cluster_size, cores)
+            ############################# 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(cluster, numbers[1], cores, numbers[3])
+                elif numbers[0] > 1 and numbers[3] >= 1:  # If unique Seconds combined multiple Firsts
+                    calc_multi_First_extended_Second_only_core(cluster, numbers[1], cores, numbers[3])
+                elif numbers[4] >= 1:
+                    Number_Of_Second_Extending_But_Same_Genomes += 1
+            else:
+                if options.verbose == True:
+                    print("First cluster " + current_cluster + " already processed - This is likely because it was clustered with another First representative.")
 
     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])
-        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])
-        elif numbers[4] >= 1:
-            Number_Of_StORF_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():
@@ -612,47 +169,73 @@ 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, cores, data[1])
         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,  cores, data[1])
     ###########################
-    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)
+    if not os.path.exists(output_path):
+        os.makedirs(output_path)
+    stats_out = os.path.join(output_path,'summary_statistics.txt')
+    key_order = list(cores.keys())
+    with open(stats_out,'w') as outfile:
+        print("Genus Groups:")
+        outfile.write("Genus Groups:\n")
+        for key in key_order:
+            print(key+':\t'+str(len(cores[key])))
+            outfile.write(key + ':\t' + str(len(cores[key]))+'\n')
+        print("Total Number of First 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.reclustered!= None:
+            print("Total Number of Second Gene Groups (Including Singletons): " + str(
+                len(combined_pangenome_clusters_Second_sequences)))
+            print("Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: " + str(
+                Number_Of_Second_Extending_But_Same_Genomes))
+            outfile.write("\nTotal Number of Second Gene Groups (Including Singletons): " + str(
+                len(combined_pangenome_clusters_Second_sequences)))
+            outfile.write("\nTotal Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: " + str(
+                Number_Of_Second_Extending_But_Same_Genomes))
 
     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')
-
-        # Create output directory if it doesn't exist
-        if not os.path.exists(output_dir):
-            os.makedirs(output_dir)
-        for key_prefix in key_order:
-            for key, values in cores.items():
-                if any(part in options.write_families.split(',') for part in key.split('_')):
-                    if key.startswith(key_prefix):
-                        for value in values:
-                            output_filename = f"{key}_{value}.fasta"
-                            sequences_to_write = pangenome_clusters_First_sequences_sorted[value]
-                            # Write sequences to output file that are in the sequences dictionary
-                            with open(os.path.join(output_dir, output_filename), 'w') as outfile:
-                                for header in sequences_to_write:
-                                    if header in sequences:
-                                        outfile.write(f">{header}\n")
-                                        wrapped_sequence = wrap_sequence(sequences[header])
-                                        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')
+        gene_presence_absence_output(options,genus_dict, pangenome_clusters_First_sorted, pangenome_clusters_First_sequences_sorted)
+
+    if options.run_mode == 'Full':
+        if options.reclustered == None:
+            combined_pangenome_clusters_Second_sequences = None
+        if options.write_groups != None:
+            print("Outputting gene group FASTA files")
+            sequences = read_fasta(options.fasta)
+            #output_dir = os.path.dirname(os.path.abspath(options.output_dir))
+            output_dir = os.path.join(options.output_dir, 'Gene_Families_Output')
+            write_groups(options,output_dir, key_order, cores, sequences,
+                         pangenome_clusters_First_sequences_sorted, combined_pangenome_clusters_Second_sequences)
+
+    elif options.run_mode == 'Partial':
+        if options.reclustered == None:
+            combined_pangenome_clusters_Second_sequences = None
+        if options.write_groups != None and options.fasta != None:
+            print("Outputting gene group FASTA files")
+            sequences = read_fasta(options.fasta)
+            #output_dir = os.path.dirname(os.path.abspath(options.output_dir))
+            output_dir = os.path.join(options.output_dir, 'Gene_Families_Output')
+            write_groups(options,output_dir, key_order, cores, sequences,
+                         pangenome_clusters_First_sequences_sorted, combined_pangenome_clusters_Second_sequences)
+
+
+    # if options.write_groups != None and options.fasta != None:
+    #     sequences = read_fasta(options.fasta)
+    #     output_dir = os.path.join(output_path, 'Gene_Families_Output')
+    #
+    #     write_groups(options,output_dir, key_order, cores, sequences,
+    #                  pangenome_clusters_First_sequences_sorted, combined_pangenome_clusters_Second_sequences)
+
+
+    #!!# - Currently only align in Species Mode
+    #if options.align_core != None and options.fasta != None and options.write_groups != None:
+    #    process_gene_families(options, os.path.join(output_path, 'Gene_Families_Output'), 'concatenated_genes_aligned.fasta')