PyamilySeq 1.3.1__tar.gz → 1.3.3__tar.gz

{pyamilyseq-1.3.1 → pyamilyseq-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyamilySeq
-Version: 1.3.1
+Version: 1.3.3
 Summary: PyamilySeq - A a tool to investigate sequence-based gene groups identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
 Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -720,7 +720,7 @@ To update to the newest version add '-U' to end of the pip install command.
 ```commandline
 usage: PyamilySeq.py [-h] {Full,Partial} ...
 
-PyamilySeq v1.3.1: A tool for gene clustering and analysis.
+PyamilySeq v1.3.3: A tool for gene clustering and analysis.
 
 positional arguments:
   {Full,Partial}  Choose a mode: 'Full' or 'Partial'.
@@ -750,7 +750,7 @@ Escherichia_coli_110957|ENSB_TIZS9kbTvShDvyX	Escherichia_coli_110957|ENSB_TIZS9k
 ```
 ### Example output:
 ```
-Running PyamilySeq v1.3.1
+Running PyamilySeq v1.3.3
 Calculating Groups
 Number of Genomes: 10
 Gene Groups
@@ -805,7 +805,7 @@ Total Number of First Gene Groups That Had Additional Second Sequences But Not N
 ## PyamilySeq is separated into two main 'run modes', Full and Partial. They each have their own set of required and optional arguments.
 ### PyamilySeq - Full Menu: 
 ```
-usage: PyamilySeq.py Full [-h] -output_dir OUTPUT_DIR -input_type {separate,combined,fasta} [-input_dir INPUT_DIR] [-input_fasta INPUT_FASTA] [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] [-sequence_type {AA,DNA}] [-gene_ident GENE_IDENT] [-c PIDENT] [-s LEN_DIFF] [-fast_mode]
+usage: PyamilySeq.py Full [-h] -output_dir OUTPUT_DIR -input_type {separate,combined,fasta} [-input_dir INPUT_DIR] [-input_fasta INPUT_FASTA] [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] [-seq_type {AA,DNA}] [-gene_ident GENE_IDENT] [-c PIDENT] [-s LEN_DIFF] [-fast_mode]
                           [-group_mode {Species,Genus}] [-species_groups SPECIES_GROUPS] [-genus_groups GENUS_GROUPS] [-write_groups WRITE_GROUPS] [-write_individual_groups] [-align] [-align_aa] [-no_gpa] [-M MEM] [-T THREADS] [-verbose] [-v]
 
 options:
@@ -821,7 +821,7 @@ options:
                         Substring to split filenames and extract genome names for gff files (e.g., '_combined.gff3') - Use with -input_type separate/combined.
   -name_split_fasta NAME_SPLIT_FASTA
                         Substring to split filenames and extract genome names for fasta files if named differently to paired gff files (e.g., '_dna.fasta') - Use with -input_type separate/combined.
-  -sequence_type {AA,DNA}
+  -seq_type {AA,DNA}
                         Clustering mode: 'DNA' or 'AA'.
   -gene_ident GENE_IDENT
                         Gene identifiers to extract sequences (e.g., 'CDS, tRNA').
@@ -895,7 +895,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split_gff .gff3 -output_dir
 ```
 usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
 
-PyamilySeq v1.3.1: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
+PyamilySeq v1.3.3: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
 
 options:
   -h, --help            show this help message and exit
@@ -927,18 +927,18 @@ Misc Arguments:
 ## Group-Splitter: This tool can split multi-copy gene groups using CD-HIT after initial PyamilySeq analysis.
 ### Example:
 ```bash
-Group-Splitter -genome_num 10 -input_fasta .../test/species/ -output_dir .../test/species/ -sequence_type AA
+Group-Splitter -genome_num 10 -input_fasta .../test/species/ -output_dir .../test/species/ -seq_type AA
 ```
 ### Group-Splitter Menu:
 ```
-usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -sequence_type {AA,DNA}
+usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -seq_type {AA,DNA}
                          -genome_num GENOME_NUM -output_dir OUTPUT_DIR
                          [-groups GROUPS] [-group_threshold GROUP_THRESHOLD]
                          [-c PIDENT] [-s LEN_DIFF] [-T CLUSTERING_THREADS]
                          [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
                          [-verbose] [-v]
 
-PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
+PyamilySeq v1.3.3: Group-Splitter - A tool to split multi-copy gene groups
 identified by PyamilySeq.
 
 options:
@@ -947,7 +947,7 @@ options:
 Required Parameters:
   -input_fasta INPUT_FASTA
                         Input FASTA file containing gene groups.
-  -sequence_type {AA,DNA}
+  -seq_type {AA,DNA}
                         Default - DNA: Are groups "DNA" or "AA" sequences?
   -genome_num GENOME_NUM
                         The total number of genomes must be provide
@@ -981,17 +981,17 @@ Misc Parameters:
 
 ```
 
-## Cluster-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
+## Group-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
 ### Example:
 ```bash
-Cluster-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
+Group-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
 ```
-### Cluster-Summary Menu: 
+### Group-Summary Menu: 
 ```
 usage: Cluster_Summary.py [-h] -input_clstr INPUT_CLSTR -output OUTPUT -genome_num GENOME_NUM
                           [-output_dir OUTPUT_DIR] [-verbose] [-v]
 
-PyamilySeq v1.3.1: Cluster-Summary - A tool to summarise CD-HIT clustering files.
+PyamilySeq v1.3.3: Group-Summary - A tool to summarise CD-HIT clustering files.
 
 options:
   -h, --help            show this help message and exit

{pyamilyseq-1.3.1 → pyamilyseq-1.3.3}/README.md

@@ -29,7 +29,7 @@ To update to the newest version add '-U' to end of the pip install command.
 ```commandline
 usage: PyamilySeq.py [-h] {Full,Partial} ...
 
-PyamilySeq v1.3.1: A tool for gene clustering and analysis.
+PyamilySeq v1.3.3: A tool for gene clustering and analysis.
 
 positional arguments:
   {Full,Partial}  Choose a mode: 'Full' or 'Partial'.
@@ -59,7 +59,7 @@ Escherichia_coli_110957|ENSB_TIZS9kbTvShDvyX	Escherichia_coli_110957|ENSB_TIZS9k
 ```
 ### Example output:
 ```
-Running PyamilySeq v1.3.1
+Running PyamilySeq v1.3.3
 Calculating Groups
 Number of Genomes: 10
 Gene Groups
@@ -114,7 +114,7 @@ Total Number of First Gene Groups That Had Additional Second Sequences But Not N
 ## PyamilySeq is separated into two main 'run modes', Full and Partial. They each have their own set of required and optional arguments.
 ### PyamilySeq - Full Menu: 
 ```
-usage: PyamilySeq.py Full [-h] -output_dir OUTPUT_DIR -input_type {separate,combined,fasta} [-input_dir INPUT_DIR] [-input_fasta INPUT_FASTA] [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] [-sequence_type {AA,DNA}] [-gene_ident GENE_IDENT] [-c PIDENT] [-s LEN_DIFF] [-fast_mode]
+usage: PyamilySeq.py Full [-h] -output_dir OUTPUT_DIR -input_type {separate,combined,fasta} [-input_dir INPUT_DIR] [-input_fasta INPUT_FASTA] [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] [-seq_type {AA,DNA}] [-gene_ident GENE_IDENT] [-c PIDENT] [-s LEN_DIFF] [-fast_mode]
                           [-group_mode {Species,Genus}] [-species_groups SPECIES_GROUPS] [-genus_groups GENUS_GROUPS] [-write_groups WRITE_GROUPS] [-write_individual_groups] [-align] [-align_aa] [-no_gpa] [-M MEM] [-T THREADS] [-verbose] [-v]
 
 options:
@@ -130,7 +130,7 @@ options:
                         Substring to split filenames and extract genome names for gff files (e.g., '_combined.gff3') - Use with -input_type separate/combined.
   -name_split_fasta NAME_SPLIT_FASTA
                         Substring to split filenames and extract genome names for fasta files if named differently to paired gff files (e.g., '_dna.fasta') - Use with -input_type separate/combined.
-  -sequence_type {AA,DNA}
+  -seq_type {AA,DNA}
                         Clustering mode: 'DNA' or 'AA'.
   -gene_ident GENE_IDENT
                         Gene identifiers to extract sequences (e.g., 'CDS, tRNA').
@@ -204,7 +204,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split_gff .gff3 -output_dir
 ```
 usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
 
-PyamilySeq v1.3.1: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
+PyamilySeq v1.3.3: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
 
 options:
   -h, --help            show this help message and exit
@@ -236,18 +236,18 @@ Misc Arguments:
 ## Group-Splitter: This tool can split multi-copy gene groups using CD-HIT after initial PyamilySeq analysis.
 ### Example:
 ```bash
-Group-Splitter -genome_num 10 -input_fasta .../test/species/ -output_dir .../test/species/ -sequence_type AA
+Group-Splitter -genome_num 10 -input_fasta .../test/species/ -output_dir .../test/species/ -seq_type AA
 ```
 ### Group-Splitter Menu:
 ```
-usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -sequence_type {AA,DNA}
+usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -seq_type {AA,DNA}
                          -genome_num GENOME_NUM -output_dir OUTPUT_DIR
                          [-groups GROUPS] [-group_threshold GROUP_THRESHOLD]
                          [-c PIDENT] [-s LEN_DIFF] [-T CLUSTERING_THREADS]
                          [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
                          [-verbose] [-v]
 
-PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
+PyamilySeq v1.3.3: Group-Splitter - A tool to split multi-copy gene groups
 identified by PyamilySeq.
 
 options:
@@ -256,7 +256,7 @@ options:
 Required Parameters:
   -input_fasta INPUT_FASTA
                         Input FASTA file containing gene groups.
-  -sequence_type {AA,DNA}
+  -seq_type {AA,DNA}
                         Default - DNA: Are groups "DNA" or "AA" sequences?
   -genome_num GENOME_NUM
                         The total number of genomes must be provide
@@ -290,17 +290,17 @@ Misc Parameters:
 
 ```
 
-## Cluster-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
+## Group-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
 ### Example:
 ```bash
-Cluster-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
+Group-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
 ```
-### Cluster-Summary Menu: 
+### Group-Summary Menu: 
 ```
 usage: Cluster_Summary.py [-h] -input_clstr INPUT_CLSTR -output OUTPUT -genome_num GENOME_NUM
                           [-output_dir OUTPUT_DIR] [-verbose] [-v]
 
-PyamilySeq v1.3.1: Cluster-Summary - A tool to summarise CD-HIT clustering files.
+PyamilySeq v1.3.3: Group-Summary - A tool to summarise CD-HIT clustering files.
 
 options:
   -h, --help            show this help message and exit

{pyamilyseq-1.3.1 → pyamilyseq-1.3.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyamilySeq"
-version = "1.3.1"
+version = "1.3.3"
 authors = [
     {name = "Nicholas Dimonaco", email = "nicholas@dimonaco.co.uk"}
 ]
@@ -33,10 +33,10 @@ Homepage = "https://github.com/NickJD/PyamilySeq"
     seq-combiner = "PyamilySeq.Seq_Combiner:main"
     Group-Splitter = "PyamilySeq.Group_Splitter:main"
     group-splitter = "PyamilySeq.Group_Splitter:main"
-    Cluster-Summary = "PyamilySeq.Cluster_Summary:main"
-    cluster-summary = "PyamilySeq.Cluster_Summary:main"
-    Cluster-Extractor = "PyamilySeq.Cluster_Extractor:main"
-    cluster-extractor = "PyamilySeq.Cluster_Extractor:main"
+    Group-Extractor = "PyamilySeq.Group_Extractor:main"
+    group-extractor = "PyamilySeq.Group_Extractor:main"
+    Group-Summary = "PyamilySeq.Group_Summary:main"
+    group-summary = "PyamilySeq.Group_Summary:main"
     Seq-Finder = "PyamilySeq.Seq_Finder:main"
     seq-finder = "PyamilySeq.Seq_Finder:main"
     Seq-Extractor = "PyamilySeq.Seq_Extractor:main"
@@ -56,5 +56,4 @@ include = ["PyamilySeq*"]
 
 [tool.setuptools.package-data]
 PyamilySeq = [
-
 ]

pyamilyseq-1.3.1/src/PyamilySeq/Cluster_Compare.py → pyamilyseq-1.3.3/src/PyamilySeq/Group_Compare.py

@@ -1,5 +1,12 @@
-import argparse
 from collections import defaultdict
+import logging
+import os
+
+# Use centralised logger factory from constants
+try:
+    from .constants import configure_logger, LoggingArgumentParser
+except Exception:
+    from constants import configure_logger, LoggingArgumentParser
 
 def read_cd_hit_output(clstr_file):
     """
@@ -23,10 +30,8 @@ def read_cd_hit_output(clstr_file):
     return seq_to_cluster
 
 def compare_cd_hit_clusters(file1, file2, output_file):
-    """
-    Compares two CD-HIT .clstr files to check if clusters are the same.
-    Writes the results to a TSV file.
-    """
+    logger = logging.getLogger("PyamilySeq.Group_Compare")
+    logger.info("Comparing clusters: %s vs %s", file1, file2)
     # Read both clustering files
     clusters1 = read_cd_hit_output(file1)
     clusters2 = read_cd_hit_output(file2)
@@ -80,12 +85,11 @@ def compare_cd_hit_clusters(file1, file2, output_file):
                     tsv_data.append([seq, cluster_id1, cluster_id2, "Cluster name change"])
 
     # Print metrics
-    print("🔢 Clustering Comparison Metrics:")
-    print(f"Cluster name changes: {cluster_name_changes}")
-    print(f"Sequence shifts (sequences assigned to different clusters): {sequence_shifts}")
-    print(f"Sequences only in the first file: {len(only_in_file1)}")
-    print(f"Sequences only in the second file: {len(only_in_file2)}")
-    print()
+    logger.info("Clustering Comparison Metrics:")
+    logger.info("Cluster name changes: %s", cluster_name_changes)
+    logger.info("Sequence shifts (sequences assigned to different clusters): %s", sequence_shifts)
+    logger.info("Sequences only in the first file: %s", len(only_in_file1))
+    logger.info("Sequences only in the second file: %s", len(only_in_file2))
 
     # Write the results to a TSV file
     with open(output_file, 'w') as out_file:
@@ -93,15 +97,25 @@ def compare_cd_hit_clusters(file1, file2, output_file):
         for row in tsv_data:
             out_file.write("\t".join(map(str, row)) + "\n")
 
-    print(f"✅ Results have been written to {output_file}")
+    logger.info("Results have been written to %s", output_file)
 
 def main():
-    parser = argparse.ArgumentParser(description="Compare two CD-HIT .clstr files to check for clustering consistency.")
+    # Early console-only logger so parser.description and argparse messages are emitted via logger
+    early_logger = configure_logger("PyamilySeq.Group_Compare", enable_file=False, log_dir=None, verbose=False)
+    parser = LoggingArgumentParser(logger_name="PyamilySeq.Group_Compare", description="Running Group-Compare - A tool to compare two CD-HIT .clstr files to check for clustering consistency.")
+
     parser.add_argument("-file1", required=True, help="First CD-HIT .clstr file")
     parser.add_argument("-file2", required=True, help="Second CD-HIT .clstr file")
     parser.add_argument("-output", required=True, help="Output file (TSV format)")
+    parser.add_argument("--log", action="store_true", dest="log", help="Create a timestamped logfile for this run.")
+    parser.add_argument("--log-dir", dest="log_dir", default=None, help="Directory for logfile (default: same dir as -output).")
     args = parser.parse_args()
 
+    # Setup logger
+    out_dir = os.path.abspath(os.path.dirname(args.output)) if args.output else os.getcwd()
+    log_dir = args.log_dir if args.log_dir else out_dir
+    logger = configure_logger("PyamilySeq.Group_Compare", enable_file=args.log, log_dir=log_dir, verbose=False)
+
     compare_cd_hit_clusters(args.file1, args.file2, args.output)
 
 if __name__ == "__main__":

{pyamilyseq-1.3.1 → pyamilyseq-1.3.3}/src/PyamilySeq/Group_Extractor.py

@@ -1,6 +1,12 @@
-import argparse
 import os
 import csv
+import logging
+
+# Use centralissed logger factory from constants
+try:
+    from .constants import configure_logger, LoggingArgumentParser
+except Exception:
+    from constants import configure_logger, LoggingArgumentParser
 
 
 def parse_fasta(fasta_file):
@@ -43,9 +49,8 @@ def parse_csv(csv_file):
 
 
 def write_group_fastas(groups, sequences, output_dir):
-    """
-    Writes individual FASTA files for each group with the relevant sequences.
-    """
+
+    logger = logging.getLogger("PyamilySeq.Group_Extractor")
     if not os.path.exists(output_dir):
         os.makedirs(output_dir)
 
@@ -56,27 +61,39 @@ def write_group_fastas(groups, sequences, output_dir):
                 if gene_id in sequences:
                     f.write(f">{gene_id}\n{sequences[gene_id]}\n")
                 else:
-                    print(f"Warning: Gene ID {gene_id} not found in FASTA file.")
+                    logger.warning("Warning: Gene ID %s not found in FASTA file.", gene_id)
 
 
 def main():
-    parser = argparse.ArgumentParser(description="Process FASTA and CSV files to create grouped FASTA outputs.")
+    # Early console-only logger so the parser description is logged before argparse outputs.
+    early_logger = configure_logger("PyamilySeq.Group_Extractor", enable_file=False, log_dir=None, verbose=False)
+    parser = LoggingArgumentParser(logger_name="PyamilySeq.Group_Extractor", description="Running Group-Extractor - A tool to process FASTA and CSV files to create grouped FASTA outputs.")
+
     parser.add_argument("-fasta", required=True, help="Input FASTA file containing gene sequences.")
     parser.add_argument("-csv", required=True, help="Input CSV file containing group and gene information.")
     parser.add_argument("-output_dir", required=True, help="Directory to save the grouped FASTA files.")
+    parser.add_argument("--log", action="store_true", dest="log", help="Create a timestamped logfile for this run.")
+    parser.add_argument("--log-dir", dest="log_dir", default=None, help="Directory for logfile (default: output_dir).")
 
     args = parser.parse_args()
 
-    # Parse the input files
-    print("Parsing FASTA file...")
+    # Setup logger writing to output_dir (optional file)
+    log_dir = os.path.abspath(args.output_dir) if args.output_dir else os.getcwd()
+    if hasattr(args, "log_dir") and args.log_dir:
+        log_dir = args.log_dir
+    # Only create a logfile when --log is provided; default is console (stdout) only.
+    logger = configure_logger("PyamilySeq.Group_Extractor", enable_file=getattr(args, "log", False), log_dir=log_dir, verbose=False)
+
+    logger.info("Parsing FASTA file: %s", args.fasta)
     sequences = parse_fasta(args.fasta)
-    print("Parsing CSV file...")
+    logger.info("Parsed %d sequences.", len(sequences))
+    logger.info("Parsing CSV file: %s", args.csv)
     groups = parse_csv(args.csv)
+    logger.info("Parsed %d groups.", len(groups))
 
-    # Write the grouped FASTA files
-    print("Writing grouped FASTA files...")
+    logger.info("Writing grouped FASTA files to %s", args.output_dir)
     write_group_fastas(groups, sequences, args.output_dir)
-    print("Process completed successfully.")
+    logger.info("Process completed successfully.")
 
 
 if __name__ == "__main__":

{pyamilyseq-1.3.1 → pyamilyseq-1.3.3}/src/PyamilySeq/Group_Sizes.py

@@ -1,6 +1,14 @@
-import argparse
+
 import os
 import csv
+import logging
+
+
+# Use centralised logger factory from constants
+try:
+    from .constants import configure_logger, LoggingArgumentParser
+except Exception:
+    from constants import configure_logger, LoggingArgumentParser
 
 
 def parse_fasta_stats(fasta_file):
@@ -43,9 +51,7 @@ def parse_fasta_stats(fasta_file):
 
 
 def process_fasta_directory(input_dir, output_csv):
-    """
-    Processes a directory of FASTA files and writes statistics to a CSV file.
-    """
+    logger = logging.getLogger("PyamilySeq.Group_Sizes")
     results = []
     for filename in os.listdir(input_dir):
         if filename.endswith(".fasta"):
@@ -68,19 +74,27 @@ def process_fasta_directory(input_dir, output_csv):
         writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
         writer.writeheader()
         writer.writerows(results)
+    logger.info("Wrote statistics for %d FASTA files to %s", len(results), output_csv)
 
 
 def main():
-    parser = argparse.ArgumentParser(description="Summarize sequence statistics for a directory of FASTA files.")
+    # Early console-only logger so the parser.description is emitted via logger before argparse prints usage/help.
+    early_logger = configure_logger("PyamilySeq.Group_Sizes", enable_file=False, log_dir=None, verbose=False)
+    parser = LoggingArgumentParser(logger_name="PyamilySeq.Group_Sizes", description="Group-Sizes - A tool to summarise sequence statistics for a directory of FASTA files.")
     parser.add_argument("-input_dir", required=True, help="Directory containing FASTA files.")
     parser.add_argument("-output_csv", required=True, help="Output CSV file to save statistics.")
+    parser.add_argument("--log", action="store_true", dest="log", help="Create a timestamped logfile for this run.")
+    parser.add_argument("--log-dir", dest="log_dir", default=None, help="Directory for logfile (default: same dir as -output_csv).")
 
     args = parser.parse_args()
 
-    # Process the directory of FASTA files
-    print("Processing FASTA files...")
+    out_dir = os.path.abspath(os.path.dirname(args.output_csv)) if args.output_csv else os.getcwd()
+    log_dir = args.log_dir if args.log_dir else out_dir
+    logger = configure_logger("PyamilySeq.Group_Sizes", enable_file=args.log, log_dir=log_dir, verbose=False)
+
+    logger.info("Processing FASTA files in %s", args.input_dir)
     process_fasta_directory(args.input_dir, args.output_csv)
-    print(f"Statistics saved to {args.output_csv}")
+    logger.info("Statistics saved to %s", args.output_csv)
 
 
 if __name__ == "__main__":