PyamilySeq 1.0.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

PyamilySeq/utils.py

@@ -0,0 +1,598 @@
+import subprocess
+import shutil
+import os
+import glob
+import collections
+from tempfile import NamedTemporaryFile
+import sys
+import re
+import math
+
+####
+# Placeholder for the distance function
+levenshtein_distance_cal = None
+# Check for Levenshtein library once
+try:
+    import Levenshtein as LV
+    # Assign the optimized function
+    def levenshtein_distance_calc(seq1, seq2):
+        return LV.distance(seq1, seq2)
+except (ModuleNotFoundError, ImportError):
+    print("Levenshtein package not installed - Will fallback to slower Python implementation.")
+    # Fallback implementation
+    def levenshtein_distance_calc(seq1, seq2):
+        # Slower Python implementation of Levenshtein distance
+        len1, len2 = len(seq1), len(seq2)
+        dp = [[0] * (len2 + 1) for _ in range(len1 + 1)]
+
+        for i in range(len1 + 1):
+            dp[i][0] = i
+        for j in range(len2 + 1):
+            dp[0][j] = j
+
+        for i in range(1, len1 + 1):
+            for j in range(1, len2 + 1):
+                if seq1[i - 1] == seq2[j - 1]:
+                    cost = 0
+                else:
+                    cost = 1
+                dp[i][j] = min(dp[i - 1][j] + 1,  # Deletion
+                               dp[i][j - 1] + 1,  # Insertion
+                               dp[i - 1][j - 1] + cost)  # Substitution
+
+        return dp[len1][len2]
+#####
+
+################### We are currently fixed using Table 11
+codon_table = {
+      'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
+      'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
+      'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
+      'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
+      'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
+      'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
+      'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
+      'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
+      'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
+      'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
+      'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
+      'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
+      'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
+      'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
+      'TAC':'Y', 'TAT':'Y', 'TAA':'*', 'TAG':'*',
+      'TGC':'C', 'TGT':'C', 'TGA':'*', 'TGG':'W'}
+
+def translate_frame(sequence):
+    translate = ''.join([codon_table.get(sequence[3 * i:3 * i + 3], 'X') for i in range(len(sequence) // 3)])
+    return translate
+
+def translate_dna_to_aa(dna_fasta, aa_fasta):
+    def translate_dna_sequence(dna_seq):
+        aa_seq = ""
+        for i in range(0, len(dna_seq) - 2, 3):
+            codon = dna_seq[i:i+3]
+            aa_seq += codon_table.get(codon, 'X')  # 'X' for unknown codons
+        return aa_seq
+
+    with open(dna_fasta, 'r') as infile, open(aa_fasta, 'w') as outfile:
+        dna_seq = ""
+        header = ""
+        for line in infile:
+            if line.startswith('>'):
+                if dna_seq:
+                    aa_seq = translate_dna_sequence(dna_seq)
+                    wrapped_aa_seq = wrap_sequence(aa_seq, 60)
+                    outfile.write(f"{header}\n{wrapped_aa_seq}\n")
+                header = line.strip()
+                dna_seq = ""
+            else:
+                dna_seq += line.strip()
+        if dna_seq:
+            aa_seq = translate_dna_sequence(dna_seq)
+            wrapped_aa_seq = wrap_sequence(aa_seq, 60)
+            outfile.write(f"{header}\n{wrapped_aa_seq}\n")
+
+
+def detect_sequence_type(fasta_file):
+    with open(fasta_file, 'r') as f:
+        for line in f:
+            if line.startswith('>'):
+                continue
+            if any(base in line for base in 'EFILPQZ'):
+                return False  # Contains amino acids
+    return True  # Contains DNA
+
+
+def is_tool_installed(tool_name):
+    """Check if a tool is installed and available in PATH."""
+    # Check if the tool is in the system PATH
+    if shutil.which(tool_name) is None:
+        return False
+
+    # Try running the tool to ensure it's executable
+    try:
+        subprocess.run([tool_name, '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
+        return True
+    except subprocess.CalledProcessError:
+        return True  # The tool is installed and ran, even if it returns an error code
+    except FileNotFoundError:
+        return False  # This shouldn't happen due to the earlier check
+
+def reverse_complement(seq):
+    complement = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G', 'N': 'N'}
+    return ''.join(complement[base] for base in reversed(seq))
+
+
+def fix_path(path):
+    fixed_path = os.path.normpath(path)
+    fixed_path = os.path.realpath(fixed_path)
+    return fixed_path
+
+
+def extract_identity(clustered_info):
+    # Use regex to capture percentage, including optional '-' or '+' before it
+    match = re.search(r'at [+-/]*(\d+\.\d+)%', clustered_info)
+
+    if match:
+        percent_identity = float(match.group(1))  # Extract the percentage value
+        return percent_identity
+    else:
+        raise ValueError("Percent identity not found in the string.")
+
+
+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_genomes_from_fasta(fasta_file):
+    genomes = set()
+    with open(fasta_file, 'r') as file:
+        for line in file:
+            line = line.strip()
+            if line.startswith('>'):
+                genome = line.split('|')[1]
+                genomes.add(genome)
+    return list(genomes)
+
+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 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, subgrouped):
+    """Select the longest sequence for each genome."""
+    longest_sequences = {}
+    for seq_id, sequence in sequences.items():
+        if subgrouped == False:
+            genome = seq_id.split('|')[0]  # Assuming genome name can be derived from the sequence ID
+        elif subgrouped == True:
+            genome = seq_id.split('|')[1]
+        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', '--thread', str(options.threads), temp_input_file_path],
+                    stdout=output_f,
+                    stderr=sys.stderr,
+                    check=True
+                )
+
+            else:
+                subprocess.run(
+                    ['mafft', '--auto', '--thread', str(options.threads), 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 read_separate_files(input_dir, name_split_gff, name_split_fasta, gene_ident, combined_out, translate):
+    paired_files_found = None
+    with open(combined_out, 'w') as combined_out_file, open(combined_out.replace('_dna.fasta','_aa.fasta'), 'w') as combined_out_file_aa:
+        gff_files = glob.glob(os.path.join(input_dir, '*' + name_split_gff))
+        if not gff_files:
+            sys.exit("Error: No GFF files found.")
+        for gff_file in gff_files:
+            genome_name = os.path.basename(gff_file).split(name_split_gff)[0]
+            if name_split_fasta == None:
+                possible_extensions = ['.fa', '.fasta', '.fna']
+                corresponding_fasta_file = None
+                for ext in possible_extensions:
+                    temp_file = os.path.splitext(gff_file)[0] + ext
+                    if os.path.exists(temp_file):
+                        corresponding_fasta_file = temp_file
+                        break
+                if corresponding_fasta_file is None:
+                    print("Corresponding FASTA file for GFF file '" + gff_file + "' not found. Skipping. - Try using the -name_split_fasta option.")
+                    continue
+            else:
+                corresponding_fasta_file = os.path.join(input_dir, genome_name + name_split_fasta)
+                if not os.path.exists(corresponding_fasta_file):
+                    print("Corresponding FASTA file for GFF file '" + gff_file + "' not found. Skipping. - Try using the -name_split_fasta option.")
+                    continue
+
+            gff_features = []
+            paired_files_found = True
+            with open(gff_file, 'r') as file:
+                seen_seq_ids = collections.defaultdict(int)
+                lines = file.readlines()
+                for line in lines:
+                    line_data = line.split('\t')
+                    if len(line_data) == 9:
+                        if any(gene_type in line_data[2] for gene_type in gene_ident):
+                            seq_id = line_data[8].split('ID=')[1].split(';')[0]
+                            contig = line_data[0]
+                            feature = line_data[2]
+                            strand = line_data[6]
+                            start, end = int(line_data[3]), int(line_data[4])
+                            if seq_id in seen_seq_ids:
+                                seq_id += '_' + str(seen_seq_ids[seq_id])
+                                seen_seq_ids[seq_id] + 1
+                            else:
+                                seen_seq_ids[seq_id] = 1
+                            gff_features.append((contig, start, end, strand, feature,  seq_id))
+            fasta_dict = collections.defaultdict(str)
+            with open(corresponding_fasta_file, 'r') as file:
+                lines = file.readlines()
+                for line in lines:
+                    if line.startswith('>'):
+                        current_contig = line[1:].split()[0]
+                        fasta_dict[current_contig] = ['', '']
+                    else:
+                        fasta_dict[current_contig][0] += line.strip()
+
+            for contig, fasta in fasta_dict.items():
+                reverse_sequence = reverse_complement(fasta[0])
+                fasta_dict[contig][1] = reverse_sequence
+
+            if fasta_dict and gff_features:
+                for contig, start, end, strand, feature, seq_id in gff_features:
+                    if contig in fasta_dict:
+                        if strand == '+':
+                            full_sequence = fasta_dict[contig][0]
+                            seq = full_sequence[start - 1:end]
+                        elif strand == '-':
+                            corrected_start = max(len(fasta_dict[contig][0]) - int(end), 1)
+                            corrected_stop = max(len(fasta_dict[contig][0]) - int(start - 1), 1)
+                            full_sequence = fasta_dict[contig][1]
+                            seq = full_sequence[corrected_start:corrected_stop]
+
+                        if translate == True:
+                            seq_aa = translate_frame(seq)
+                            wrapped_sequence_aa = '\n'.join([seq_aa[i:i + 60] for i in range(0, len(seq_aa), 60)])
+                            combined_out_file_aa.write(f">{genome_name}|{seq_id}\n{wrapped_sequence_aa}\n")
+                        wrapped_sequence = '\n'.join([seq[i:i + 60] for i in range(0, len(seq), 60)])
+                        combined_out_file.write(f">{genome_name}|{seq_id}\n{wrapped_sequence}\n")
+
+    if not paired_files_found:
+        sys.exit("Could not find matching GFF/FASTA files - Please check input directory and -name_split_gff and -name_split_fasta parameters.")
+    if translate == False or translate == None:
+        #Clean up unused file
+        if combined_out_file.name != combined_out_file_aa.name:
+            os.remove(combined_out_file_aa.name)
+
+
+def read_combined_files(input_dir, name_split, gene_ident, combined_out, translate):
+    with open(combined_out, 'w') as combined_out_file, open(combined_out.replace('_dna.fasta','_aa.fasta'), 'w') as combined_out_file_aa:
+        gff_files = glob.glob(os.path.join(input_dir, '*' + name_split))
+        if not gff_files:
+            sys.exit("Error: No GFF files found - check input directory and -name_split_gff parameter.")
+        for gff_file in gff_files:
+            genome_name = os.path.basename(gff_file).split(name_split)[0]
+            fasta_dict = collections.defaultdict(str)
+            gff_features = []
+            with open(gff_file, 'r') as file:
+                seen_seq_ids = collections.defaultdict(int)
+                lines = file.readlines()
+                fasta_section = False
+                for line in lines:
+                    if line.startswith('##FASTA'):
+                        fasta_section = True
+                        continue
+                    if fasta_section:
+                        if line.startswith('>'):
+                            current_contig = line[1:].split()[0]
+                            fasta_dict[current_contig] = ['','']
+                        else:
+                            fasta_dict[current_contig][0] +=line.strip()
+                    else:
+                        line_data = line.split('\t')
+                        if len(line_data) == 9:
+                            if any(gene_type in line_data[2] for gene_type in gene_ident):
+                                contig = line_data[0]
+                                feature = line_data[2]
+                                strand = line_data[6]
+                                start, end = int(line_data[3]), int(line_data[4])
+                                seq_id = line_data[8].split('ID=')[1].split(';')[0]
+                                if seq_id in seen_seq_ids:
+                                    seq_id += '_' + str(seen_seq_ids[seq_id])
+                                    seen_seq_ids[seq_id] + 1
+                                else:
+                                    seen_seq_ids[seq_id] = 1
+                                gff_features.append((contig, start, end, strand, feature,  seq_id))
+
+                for contig, fasta in fasta_dict.items():
+                    reverse_sequence = reverse_complement(fasta[0])
+                    fasta_dict[contig][1]=reverse_sequence
+
+                if fasta_dict and gff_features:
+                    for contig, start, end, strand, feature, seq_id in gff_features:
+                        if contig in fasta_dict:
+                            if strand == '+':
+                                full_sequence = fasta_dict[contig][0]
+                                seq = full_sequence[start - 1:end]
+                            elif strand == '-':
+                                corrected_start = max(len(fasta_dict[contig][0]) - int(end), 1)
+                                corrected_stop = max(len(fasta_dict[contig][0]) - int(start - 1), 1)
+                                full_sequence = fasta_dict[contig][1]
+                                seq = full_sequence[corrected_start:corrected_stop]
+
+                            if translate == True:
+                                seq_aa = translate_frame(seq)
+                                wrapped_sequence_aa = '\n'.join([seq_aa[i:i + 60] for i in range(0, len(seq_aa), 60)])
+                                combined_out_file_aa.write(f">{genome_name}|{seq_id}\n{wrapped_sequence_aa}\n")
+                            wrapped_sequence = '\n'.join([seq[i:i + 60] for i in range(0, len(seq), 60)])
+                            combined_out_file.write(f">{genome_name}|{seq_id}\n{wrapped_sequence}\n")
+
+    if translate == False or translate == None:
+        #Clean up unused file
+        if combined_out_file.name != combined_out_file_aa.name:
+            os.remove(combined_out_file_aa.name)
+
+
+
+def read_fasta_files(input_dir, name_split_fasta, combined_out, translate):
+    with open(combined_out, 'w') as combined_out_file, open(combined_out.replace('_dna.fasta','_aa.fasta'), 'w') as combined_out_file_aa:
+        fasta_files = glob.glob(os.path.join(input_dir, '*' + name_split_fasta))
+        if not fasta_files:
+            sys.exit("Error: No GFF files found.")
+        for fasta_file in fasta_files:
+            genome_name = os.path.basename(fasta_file).split(name_split_fasta)[0]
+            fasta_dict = collections.defaultdict(str)
+            with open(fasta_file, 'r') as file:
+                lines = file.readlines()
+                for line in lines:
+                    if line.startswith('>'):
+                        current_seq = line[1:].split()[0]
+                        fasta_dict[current_seq] = ''
+                    else:
+                        fasta_dict[current_seq] +=line.strip()
+                for seq_id, seq in fasta_dict.items():
+                    if translate == True:
+                        seq_aa = translate_frame(seq)
+                        wrapped_sequence_aa = '\n'.join([seq_aa[i:i + 60] for i in range(0, len(seq_aa), 60)])
+                        combined_out_file_aa.write(f">{genome_name}|{seq_id}\n{wrapped_sequence_aa}\n")
+                    wrapped_sequence = '\n'.join([seq[i:i + 60] for i in range(0, len(seq), 60)])
+                    combined_out_file.write(f">{genome_name}|{seq_id}\n{wrapped_sequence}\n")
+
+    if translate == False or translate == None:
+        #Clean up unused file
+        if combined_out_file.name != combined_out_file_aa.name:
+            os.remove(combined_out_file_aa.name)
+
+def write_groups_func(options, output_dir, key_order, cores, sequences,
+                 pangenome_clusters_First_sequences_sorted, combined_pangenome_clusters_Second_sequences):
+    """
+    Writes individual FASTA files and a combined FASTA file for all sequences.
+
+    Parameters:
+    - options: Command-line options.
+    - output_dir: Directory where output FASTA files will be saved.
+    - key_order: The order in which to process keys.
+    - cores: Dictionary of core genes.
+    - sequences: Dictionary mapping headers to sequences.
+    - pangenome_clusters_First_sequences_sorted: Dictionary of first sequence clusters.
+    - combined_pangenome_clusters_Second_sequences: Dictionary of second sequence clusters.
+    """
+    # Create output directory if it doesn't exist
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    for group in options.write_groups.split(','):
+
+        combined_fasta_filename = os.path.join(output_dir, "combined_group_sequences_" + group + "_dna.fasta")
+
+        # Open combined FASTA file for writing all sequences
+        with open(combined_fasta_filename, 'w') as combined_fasta, open(combined_fasta_filename.replace('_dna.fasta','_aa.fasta'), 'w') as combined_fasta_aa:
+            for key_prefix in key_order:
+                for key, values in cores.items():
+                    if any(part in group for part in key.split('_')):
+                        if key.startswith(key_prefix):
+                            for value in values:
+                                output_filename = f"{key}_{value}_dna.fasta"
+                                if 'First' in key_prefix:
+                                    sequences_to_write = pangenome_clusters_First_sequences_sorted[value]
+                                else:
+                                    sequences_to_write = combined_pangenome_clusters_Second_sequences[value]
+
+                                # Write individual FASTA file
+                                with open(os.path.join(output_dir,output_filename), 'w') as outfile, open(os.path.join(output_dir, output_filename.replace('_dna.fasta','_aa.fasta')), 'w') as outfile_aa:
+                                    for header in sequences_to_write:
+                                        if header in sequences:
+                                            sequence = sequences[header]
+                                            wrapped_sequence = wrap_sequence(sequence)
+                                            # Handle Amino Acid Sequences (AA)
+                                            if options.sequence_type == 'AA':
+                                                seq_aa = translate_frame(sequence)
+                                                wrapped_sequence_aa = wrap_sequence(seq_aa)
+                                                # Write individual group file for AA, if option is enabled
+                                                if options.write_individual_groups:
+                                                    outfile_aa.write(f">{header}\n")
+                                                    outfile_aa.write(f"{wrapped_sequence_aa}\n")
+                                                else:
+                                                    os.remove(outfile_aa.name)  # Delete individual file if option is disabled
+                                                # Always write to the combined AA file
+                                                combined_fasta_aa.write(f">Group_{value}|{header}\n")
+                                                combined_fasta_aa.write(f"{wrapped_sequence_aa}\n")
+                                            # Handle Nucleotide Sequences
+                                            else:
+                                                # If the option is disabled, delete individual AA file (if created)
+                                                try:
+                                                    os.remove(outfile_aa.name)  # Ensure outfile_aa is removed when sequence_type isn't 'AA'
+                                                except FileNotFoundError:
+                                                    pass
+                                            # Write individual group file for nucleotide sequence, if option is enabled
+                                            if options.write_individual_groups:
+                                                outfile.write(f">{header}\n")
+                                                outfile.write(f"{wrapped_sequence}\n")
+                                            else:
+                                                os.remove(outfile.name)  # Delete individual file if option is disabled
+                                            # Always write to the combined nucleotide file
+                                            combined_fasta.write(f">Group_{value}|{header}\n")
+                                            combined_fasta.write(f"{wrapped_sequence}\n")
+
+                                        else:
+                                            if options.verbose == True:
+                                                print(f"Sequence {header} not found in original_fasta file.")
+        if options.sequence_type != 'AA':
+            #Clean up unused file
+            os.remove(combined_fasta_aa.name)
+    print(f"Combined FASTA file saved to: {combined_fasta_filename}")
+
+
+# def process_gene_groups(options, group_directory, sub_group_directory, paralog_groups, output_file):
+#     """Process each gene family file to select the longest sequence per genome and concatenate aligned sequences."""
+#     concatenated_sequences = {}
+#     output_file = group_directory.replace('Gene_Groups_Output',output_file)
+#
+#     # Iterate over each gene family file
+#     for gene_file in os.listdir(group_directory):
+#         if gene_file.endswith('.fasta') and not gene_file.endswith('combined_group_sequences.fasta') :
+#             gene_path = os.path.join(group_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"{group_directory}/{gene_file}_aligned.fasta.tmp"
+#             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 perform_alignment(gene_path,group_directory, gene_file, options, concatenated_sequences, subgrouped):
+    # 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, subgrouped)
+
+    # Run mafft on the longest sequences
+    aligned_file = f"{group_directory}/{gene_file}_aligned.fasta.tmp"
+    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)
+    # Find the length of the longest sequence in aligned_sequences
+    max_length = max(len(seq) for seq in aligned_sequences.values())
+
+    for genome, sequence in concatenated_sequences.items():
+        if any(genome in key for key in aligned_sequences.keys()):
+            genome_name_in_aligned = next(key for key in aligned_sequences.keys() if genome in key)#.split('|')[split_by]
+            concatenated_sequences[genome] += aligned_sequences[genome_name_in_aligned]
+        else:
+            concatenated_sequences[genome] += "-" * max_length
+
+    # Clean up aligned file
+    os.remove(aligned_file)
+
+    return concatenated_sequences
+
+def process_gene_groups(options, group_directory, sub_group_directory, paralog_groups, genome_list, output_file):
+    """Process each gene family file to select the longest sequence per genome and concatenate aligned sequences."""
+    concatenated_sequences = {genome: "" for genome in genome_list}
+    output_file = group_directory.replace('Gene_Groups_Output', output_file)
+    if paralog_groups != None:
+        threshold_size = math.floor(int(options.align_core) * int(options.genome_num) / 100)
+
+    if options.align_aa == True:
+        affix = '_aa.fasta'
+    else:
+        affix = '_dna.fasta'
+
+    if options.align_core == True:
+        # Iterate over each gene family file
+        for gene_file in os.listdir(group_directory):
+            if gene_file.endswith(affix) and not gene_file.startswith('combined_group_sequences'):
+                #print(gene_file)
+                current_group = int(gene_file.split('_')[3].split('.')[0])
+                gene_path = os.path.join(group_directory, gene_file)
+
+                # Check for matching group in paralog_groups
+                if sub_group_directory and paralog_groups and '>Group_'+str(current_group) in paralog_groups:
+                    for subgroup, size in enumerate(paralog_groups['>Group_' + str(current_group)]['sizes']):
+                        if size >= threshold_size:
+                            gene_path = os.path.join(sub_group_directory,f"Group_{current_group}_subgroup_{subgroup}{affix}")
+                            concatenated_sequences = perform_alignment(gene_path, group_directory, gene_file, options, concatenated_sequences, True)
+
+                else:
+                    concatenated_sequences = perform_alignment(gene_path, group_directory, gene_file, options, concatenated_sequences, False)
+
+
+    # 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")
+