mgnify-pipelines-toolkit 0.2.1__py3-none-any.whl → 1.0.0__py3-none-any.whl

mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_matching.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the 'License');
 # you may not use this file except in compliance with the License.

mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py

@@ -0,0 +1,511 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the 'License');
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an 'AS IS' BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+import json
+import logging
+from collections import defaultdict
+import csv
+import re
+
+from intervaltree import Interval, IntervalTree
+from Bio import SeqIO
+
+
+MASK_OVERLAP_THRESHOLD = 5
+
+
+def parse_gff(gff_file):
+    """
+    Parse a GFF file and extract CDS features as Interval objects.
+
+    Args:
+        gff_file (str): Path to the GFF file.
+
+    Returns:
+        dict: A nested dictionary with sequence IDs as keys, and within each,
+            strand (+/-) as keys, containing a list of Intervals for CDS regions.
+            Each Interval object apart from the start and end positions of the CDS region
+            also stores the protein ID.
+    """
+    predictions = defaultdict(lambda: defaultdict(list))
+    with open(gff_file, "r") as gff_in:
+        for line in gff_in:
+            if line.startswith("#"):
+                continue
+            fields = line.strip().split("\t")
+            seq_id, _, feature_type, start, end, _, strand, _, attributes = fields
+            if feature_type == "CDS":
+                # Parse attributes to get the ID value
+                attr_dict = dict(
+                    attr.split("=") for attr in attributes.split(";") if "=" in attr
+                )
+                protein_id = attr_dict["ID"]
+                predictions[seq_id][strand].append(
+                    Interval(int(start), int(end), data={"protein_id": protein_id})
+                )
+    if not predictions:
+        raise ValueError("Zero gene predictions was read from the GFF file")
+    return predictions
+
+
+def parse_pyrodigal_output(file):
+    """
+    Parse Pyrodigal *.out file to extract gene predictions as Interval objects.
+    Example of *.out file:
+    # Sequence Data: seqnum=1;seqlen=25479;seqhdr="Bifidobacterium-longum-subsp-infantis-MC2-contig1"
+    # Model Data: version=Pyrodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=59.94;transl_table=11;uses_sd=1
+    >1_1_279_+
+
+    Args:
+        file (str): Path to the Pyrodigal *.out file.
+
+    Returns:
+        dict: A nested dictionary with sequence IDs as keys, and within each,
+            strand (+/-) as keys, containing a list of Intervals for CDS regions.
+            Each Interval object apart from the start and end positions of the CDS region
+            also stores the protein ID.
+    """
+    predictions = defaultdict(lambda: defaultdict(list))
+    with open(file) as file_in:
+        for line in file_in:
+            if line.startswith("# Model Data"):
+                continue
+            if line.startswith("# Sequence Data"):
+                matches = re.search(r'seqhdr="(\S+)"', line)
+                if matches:
+                    seq_id = matches.group(1)
+            else:
+                fields = line[1:].strip().split("_")
+                # Fragment_id is an index of the fragment
+                # Pyrodigal uses these (rather than coordinates) to identify sequences in the fasta output
+                fragment_id, start, end, strand = fields
+                protein_id = f"{seq_id}_{fragment_id}"
+                predictions[seq_id][strand].append(
+                    Interval(int(start), int(end), data={"protein_id": protein_id})
+                )
+    if not predictions:
+        raise ValueError("Zero gene predictions was read from the *.out file")
+    return predictions
+
+
+def parse_fgsrs_output(file):
+    """
+    Parse FragGeneScanRS *.out file to extract gene predictions as Interval objects.
+    Example of *.out file:
+    >Bifidobacterium-longum-subsp-infantis-MC2-contig1
+    256	2133	-	1	1.263995	I:	D:
+
+    Args:
+        file (str): Path to the FragGeneScanRS *.out file.
+
+    Returns:
+        dict: A nested dictionary with sequence IDs as keys, and within each,
+            strand (+/-) as keys, containing a list of Intervals for CDS regions.
+            Each Interval object apart from the start and end positions of the CDS region
+            also stores the protein ID.
+    """
+    predictions = defaultdict(lambda: defaultdict(list))
+    with open(file) as file_in:
+        for line in file_in:
+            if line.startswith(">"):
+                seq_id = line.split()[0][1:]
+            else:
+                fields = line.strip().split("\t")
+                start, end, strand, *_ = fields
+                protein_id = f"{seq_id}_{start}_{end}_{strand}"
+                predictions[seq_id][strand].append(
+                    Interval(int(start), int(end), data={"protein_id": protein_id})
+                )
+    if not predictions:
+        raise ValueError("Zero gene predictions was read from the *.out file")
+    return predictions
+
+
+def parse_cmsearch_output(mask_file):
+    """
+    Parse masking regions from a cmsearch output file and store them as Intervals.
+
+    Args:
+        mask_file (str): Path to the masking file (possibly BED or GFF-like format).
+
+    Returns:
+        dict: A dictionary with sequence IDs as keys, and a list of Intervals representing masked regions.
+    """
+    regions = defaultdict(list)
+    with open(mask_file) as file_in:
+        for line in file_in:
+            if line.startswith("#"):
+                continue
+            fields = line.rstrip().split()
+            seq_id = fields[0]
+            start = int(fields[7])
+            end = int(fields[8])
+            if start > end:
+                start, end = end, start
+            regions[seq_id].append(Interval(start, end))
+    if not regions:
+        raise ValueError("Zero intervals was read from the input masking file")
+    return regions
+
+
+def mask_regions(predictions, mask):
+    """
+    Apply masking to predictions by removing regions that overlap significantly
+    (more than MASK_OVERLAP_THRESHOLD)
+    with masked regions.
+
+    Args:
+        predictions (dict): A nested dictionary with sequence IDs as keys, and within each,
+            strand (+/-) as keys, containing a list of Intervals as values.
+        mask (dict): A dictionary with sequence IDs as keys, and a list of Intervals as values.
+
+    Returns:
+        dict: Updated predictions with masked regions removed.
+    """
+    masked = defaultdict(lambda: defaultdict(list))
+
+    for seq_id, strand_dict in predictions.items():
+        if seq_id in mask:
+            mask_tree = create_interval_tree(mask[seq_id])
+            for strand, regions in strand_dict.items():
+                tree = create_interval_tree(regions)
+                masked_intervals = []
+                for region in tree:
+                    # Check for overlaps greater than 5 base pairs
+                    overlapping_intervals = mask_tree.overlap(region.begin, region.end)
+                    overlap = False
+                    for mask_region in overlapping_intervals:
+                        # If overlap is more than 5 base pairs, mark for masking
+                        # Add 1 to make boundaries inclusive
+                        overlap_len = 1 + abs(
+                            min(region.end, mask_region.end)
+                            - max(region.begin, mask_region.begin)
+                        )
+                        if overlap_len > MASK_OVERLAP_THRESHOLD:
+                            overlap = True
+                            break
+                    if not overlap:
+                        masked_intervals.append(region)
+                masked[seq_id][strand] = sorted(masked_intervals)
+        else:
+            # If no mask information exists, add the predictions directly
+            masked[seq_id] = strand_dict
+    return masked
+
+
+def merge_predictions(predictions, priority):
+    """
+    Merge gene predictions from two sources, applying a priority order.
+
+    Args:
+        predictions (dict): Nested dictionary containing gene predictions from both sources.
+        priority (list): List specifying the order of priority for merging the predictions.
+
+    Returns:
+        dict: Nested dictionary with all predictions of the first priority source merged with non-overlapping predictions
+            the secondary source.
+    """
+    merged = defaultdict(lambda: defaultdict((lambda: defaultdict(list))))
+    primary, secondary = priority
+
+    # Primary merge
+    merged[primary] = predictions[primary]
+
+    # Secondary merge: add non-overlapping regions from the secondary gene caller
+    for seq_id in predictions[secondary]:
+        for strand in ["+", "-"]:
+            secondary_regions = predictions[secondary][seq_id][strand]
+            if seq_id in predictions[primary]:
+                primary_regions = merged[primary][seq_id][strand]
+                merged[secondary][seq_id][strand].extend(
+                    check_against_gaps(primary_regions, secondary_regions)
+                )
+            else:
+                merged[secondary][seq_id][strand] = secondary_regions
+    return merged
+
+
+def check_against_gaps(regions, candidates):
+    """
+    Check candidate regions against existing regions and select those
+    that do not overlap with any existing ones.
+
+    Args:
+        regions (list): Interval objects for existing regions.
+        candidates (list): Interval objects for candidate regions.
+
+    Returns:
+        list: Selected candidate Intervals that do not overlap with existing ones.
+    """
+    regions_tree = create_interval_tree(regions)
+    selected_candidates = []
+    for candidate in candidates:
+        # Check if the candidate overlaps with any existing region
+        if not regions_tree.overlap(candidate.begin, candidate.end):
+            selected_candidates.append(candidate)
+    return selected_candidates
+
+
+def output_fasta_files(predictions, files_dict, output_faa, output_ffn):
+    """
+    Write FASTA output files containing protein and transcript sequences for
+    the predicted genes after merging.
+
+    Args:
+        predictions (dict): Nested dictionary with merged gene predictions as Interval objects.
+            Each Interval object stores a protein ID in the data attribute.
+        files_dict (dict): Dictionary containing input FASTA files for both Pyrodigal and FragGeneScanRS.
+        output_faa (str): Path to output protein FASTA file.
+        output_ffn (str): Path to output transcript FASTA file.
+    """
+    with (
+        open(output_faa, "w") as output_faa_fh,
+        open(output_ffn, "w") as output_ffn_fh,
+    ):
+        for caller, seq_data in predictions.items():
+            proteins = set()
+            for seq_id, strand_dict in seq_data.items():
+                for strand, regions in strand_dict.items():
+                    for region in regions:
+                        protein_id = region.data["protein_id"]
+                        proteins.add(protein_id)
+
+            for input_file, output_file in [
+                (files_dict[caller]["proteins"], output_faa_fh),
+                (files_dict[caller]["transcripts"], output_ffn_fh),
+            ]:
+                sequences = []
+                for record in SeqIO.parse(input_file, "fasta"):
+                    if record.id in proteins:
+                        # Prodigal appends * to the end of a truncated sequence
+                        # FGS uses * to mark an ambiguous amino acid
+                        # Replace ending * and replace any other "*" with "X"
+                        record.seq = record.seq.rstrip("*").replace("*", "X")
+                        sequences.append(record)
+                SeqIO.write(sequences, output_file, "fasta")
+
+
+def output_gff(predictions, output_gff):
+    """
+    Write merged gene predictions to a GFF output file.
+
+    Args:
+        predictions (dict): Nested dictionary with merged gene predictions as Interval objects.
+            Each Interval object stores a protein ID in the data attribute.
+        output_gff (str): Path to the output GFF file.
+    """
+    with open(output_gff, "w") as gff_out:
+        writer = csv.writer(gff_out, delimiter="\t")
+        gff_out.write("##gff-version 3\n")
+        for caller, seq_data in predictions.items():
+            for seq_id, strand_dict in seq_data.items():
+                for strand, regions in strand_dict.items():
+                    for region in regions:
+                        writer.writerow(
+                            [
+                                seq_id,  # Sequence ID
+                                caller,  # Source
+                                "CDS",  # Feature type
+                                region.begin,  # Start position
+                                region.end,  # End position
+                                ".",  # Score (not used, hence '.')
+                                strand,  # Strand (+/-)
+                                ".",  # Phase (not used, hence '.')
+                                f"ID={region.data['protein_id']}",  # Attributes
+                            ]
+                        )
+
+
+def output_summary(summary, output_file):
+    """
+    Write a summary of gene counts to a text file in JSON format.
+
+    Args:
+        summary (dict): Summary of gene counts.
+        output_file (str): Path to the summary output file.
+    """
+    with open(output_file, "w") as sf:
+        sf.write(json.dumps(summary, sort_keys=True, indent=4) + "\n")
+
+
+def get_counts(predictions):
+    """
+    Count the number of gene predictions for each caller.
+
+    Args:
+        predictions (dict): Nested dictionary with gene predictions for each caller.
+
+    Returns:
+        dict: Total count of genes for each caller.
+    """
+    total = {}
+    for caller, seq_data in predictions.items():
+        count = sum(
+            len(seq_data[seq_id]["+"] + seq_data[seq_id]["-"]) for seq_id in seq_data
+        )
+        total[caller] = count
+    return total
+
+
+def create_interval_tree(regions):
+    """
+    Create an IntervalTree from a list of regions.
+
+    Args:
+        regions (list): List of Interval objects.
+
+    Returns:
+        IntervalTree: An interval tree for efficient overlap checking.
+    """
+    tree = IntervalTree()
+    for region in regions:
+        tree.add(region)
+    return tree
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        """
+        MGnify gene caller combiner.
+        This script merges gene predictions made by Pyrodigal and FragGeneScanRS (FGS)
+        and outputs FASTA and GFF files.
+        For each gene caller, the script expects a set of files:
+        - GFF file with gene predictions OR *.out file
+        - FASTA file with protein sequences
+        - FASTA file with transcript sequences
+        """
+    )
+    parser.add_argument(
+        "--name", "-n", required=True, help="Base name for output files"
+    )
+    parser.add_argument(
+        "--priority",
+        "-P",
+        choices=["Pyrodigal_FragGeneScanRS", "FragGeneScanRS_Pyrodigal"],
+        default="Pyrodigal_FragGeneScanRS",
+        help="Merge priority",
+    )
+    parser.add_argument(
+        "--mask",
+        "-m",
+        help="Regions for masking (Infernal cmsearch output file)",
+    )
+    parser.add_argument("--pyrodigal-gff", "-pg", help="Pyrodigal *.gff file")
+    parser.add_argument("--pyrodigal-out", "-po", help="Pyrodigal *.out file")
+    parser.add_argument(
+        "--pyrodigal-ffn",
+        "-pt",
+        required=True,
+        help="Pyrodigal *.ffn file with transcripts",
+    )
+    parser.add_argument(
+        "--pyrodigal-faa",
+        "-pp",
+        required=True,
+        help="Pyrodigal *.faa file with proteins",
+    )
+    parser.add_argument("--fgsrs-gff", "-fg", help="FragGeneScanRS *.gff file")
+    parser.add_argument("--fgsrs-out", "-fo", help="FragGeneScanRS *.out file")
+    parser.add_argument(
+        "--fgsrs-ffn",
+        "-ft",
+        required=True,
+        help="FragGeneScanRS *.ffn file with transcripts",
+    )
+    parser.add_argument(
+        "--fgsrs-faa",
+        "-fp",
+        required=True,
+        help="FragGeneScanRS *.faa file with proteins",
+    )
+    parser.add_argument(
+        "--verbose", "-v", action="store_true", help="Increase verbosity level to debug"
+    )
+    args = parser.parse_args()
+
+    log_level = logging.DEBUG if args.verbose else logging.INFO
+    logging.basicConfig(
+        level=log_level,
+        format="%(levelname)s %(asctime)s - %(message)s",
+        datefmt="%Y/%m/%d %H:%M:%S",
+    )
+
+    if not args.pyrodigal_out and not args.pyrodigal_gff:
+        parser.error(
+            "For Pyrodigal, you must provide either --pyrodigal-out or --pyrodigal-gff"
+        )
+
+    if not args.fgsrs_out and not args.fgsrs_gff:
+        parser.error(
+            "For FragGeneScanRS, you must provide either --fgsrs-out or --fgsrs-gff"
+        )
+
+    summary = {}
+    all_predictions = {}
+
+    caller_priority = args.priority.split("_")
+    logging.info(f"Caller priority: 1. {caller_priority[0]}, 2. {caller_priority[1]}")
+
+    logging.info("Parsing Pyrodigal annotations...")
+    if args.pyrodigal_out:
+        all_predictions["Pyrodigal"] = parse_pyrodigal_output(args.pyrodigal_out)
+    elif args.pyrodigal_gff:
+        all_predictions["Pyrodigal"] = parse_gff(args.pyrodigal_gff)
+
+    logging.info("Parsing FragGeneScanRS annotations...")
+    if args.fgsrs_out:
+        all_predictions["FragGeneScanRS"] = parse_fgsrs_output(args.fgsrs_out)
+    elif args.fgsrs_gff:
+        all_predictions["FragGeneScanRS"] = parse_gff(args.fgsrs_gff)
+
+    summary["all"] = get_counts(all_predictions)
+
+    if args.mask:
+        logging.info("Masking of non-coding RNA regions was enabled")
+        logging.info(f"Parsing masking intervals from file {args.mask}")
+        mask_regions_file = parse_cmsearch_output(args.mask)
+        for caller in all_predictions:
+            logging.info(f"Masking {caller} outputs...")
+            all_predictions[caller] = mask_regions(
+                all_predictions[caller], mask_regions_file
+            )
+        summary["after_masking"] = get_counts(all_predictions)
+
+    logging.info("Merging combined gene caller results")
+    merged_predictions = merge_predictions(all_predictions, caller_priority)
+    summary["merged"] = get_counts(merged_predictions)
+
+    logging.info("Writing output files...")
+    output_summary(summary, f"{args.name}.summary.txt")
+    output_gff(merged_predictions, f"{args.name}.gff")
+    files = {
+        "Pyrodigal": {
+            "proteins": args.pyrodigal_faa,
+            "transcripts": args.pyrodigal_ffn,
+        },
+        "FragGeneScanRS": {"proteins": args.fgsrs_faa, "transcripts": args.fgsrs_ffn},
+    }
+    output_fasta_files(
+        merged_predictions,
+        files,
+        f"{args.name}.faa",
+        f"{args.name}.ffn",
+    )
+
+
+if __name__ == "__main__":
+    main()

mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2024 EMBL - European Bioinformatics Institute
+# Copyright 2024-2025 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the 'License');
 # you may not use this file except in compliance with the License.