MetaPont 0.1.0__tar.gz → 0.1.2__tar.gz

metapont-0.1.2/PKG-INFO

@@ -0,0 +1,224 @@
+Metadata-Version: 2.4
+Name: MetaPont
+Version: 0.1.2
+Summary: Integrated analysis of metagenomic assembly, readmapping, Kraken2 and eggNOG-mapper outputs.
+Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/TheHuwsLab/MetaPont
+Project-URL: Bug Tracker, https://github.com/TheHuwsLab/MetaPont/issues
+Keywords: metagenomics,bioinformatics,genomics,Kraken2,eggNOG-mapper,readmapping
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: plots
+Requires-Dist: matplotlib>=3.7; extra == "plots"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Dynamic: license-file
+
+# MetaPont v0.1.2
+
+MetaPont integrates existing metagenomic workflow outputs into per-sample and
+cross-sample tables for contigs, taxonomy, readmapping support, and eggNOG-mapper
+functional annotations. It is designed for outputs from the
+[HuwsLab Metagenomic Workflow](https://github.com/TheHuwsLab/Metagenomic_Workflow),
+but does not run assembly, readmapping, Kraken2, or eggNOG-mapper itself.
+
+## Installation
+
+MetaPont requires Python 3.10 or later and has no required third-party runtime
+dependencies.
+
+```bash
+pip install MetaPont
+```
+
+Check the installed version and available commands with:
+
+```bash
+metapont --version
+metapont --help
+```
+
+## Input layout
+
+Pass MetaPont the directory containing sample directories. Sample directories
+are selected when their names start with one of the comma-separated prefixes
+provided with `--prefix`.
+
+```text
+workflow-output/
+├── E1.0/
+│   ├── E1.0_metaspades/contigs.fasta
+│   ├── E1.0_pyrodigal/
+│   ├── E1.0_eggnog_mapper/
+│   │   └── E1.0_pyrodigal_eggnog_mapped.emapper.annotations
+│   ├── E1.0_kraken2/
+│   │   ├── E1.0_kraken2.txt
+│   │   └── E1.0_kraken2_report.txt
+│   └── E1.0_readmapped/
+│       ├── E1.0_readmapped_contig_summary.txt
+│       └── E1.0_readmapped_cds_summary.txt
+└── E2.0/
+    └── ...
+```
+
+MetaPont discovers common workflow naming variants and searches within each
+sample directory for the relevant files. The main inputs are:
+
+| Input | Used for |
+| --- | --- |
+| eggNOG-mapper `.emapper.annotations` | Gene annotations and functional features |
+| Kraken2 contig classifications and report | Contig taxonomic assignments and lineages |
+| Readmapping contig summary | Contig lengths, mapped-read counts, and mapping proportions |
+| Readmapping CDS summary | Read support attributed to annotated genes |
+| Contig FASTA | Contig inventory and lengths when a readmapping contig summary is absent |
+
+Inputs are discovered independently, so incomplete samples can still be
+included. Missing or stale outputs are reported as warnings; MetaPont does not
+rerun missing upstream analyses. Kraken2 assignments shorter than the selected
+minimum contig length are omitted from taxonomy attribution by default. This
+filter does not rerun Kraken2.
+
+## Commands
+
+### Build integrated results
+
+```bash
+metapont run \
+  --root-dir /path/to/workflow-output \
+  --prefix E
+```
+
+`--prefix` accepts comma-separated values, for example `E,L,P`. By default,
+results are written under `ROOT/MetaPont_Results`. Override that location with
+`--output-dir`.
+
+Useful options:
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--force` | Off | Regenerate outputs even when the input signature matches a cached run. |
+| `--no-heal-flags` | Off | Do not recreate missing upstream success flags when their outputs are complete and current. |
+| `--min-contig-length N` | `2500` | Minimum Kraken2-assigned contig length retained for taxonomy attribution; use `0` to disable the filter. |
+| `--taxon-function-abundance` | Off | Build the expanded taxon-by-function table. This can use substantial memory and disk space. |
+| `--plots` | Off | Write optional quick-look PNG plots. Requires the `plots` installation extra. |
+
+`metapont combine` is an alias for `metapont run`. The `metapont-combine`
+command is also available for compatibility with the earlier combine command.
+
+### Audit sample inputs
+
+```bash
+metapont inventory --root-dir /path/to/workflow-output --prefix E
+```
+
+The inventory reports discovered inputs, expected outputs, success flags, and
+warnings for each sample. Add `--heal-flags` to recreate a missing stage flag
+only when its corresponding output files are complete and current.
+
+### Summarise readmapping coverage
+
+```bash
+metapont coverage \
+  --root-dir /path/to/workflow-output \
+  --prefix E \
+  --read-length 150
+```
+
+The optional read length adds an approximate mapped-read coverage estimate.
+Without `--output`, the TSV is written to
+`MetaPont_Results/summary/contig_coverage_summary.tsv`.
+
+### Query functions and taxa
+
+Find taxa supporting a functional ID:
+
+```bash
+metapont query-function \
+  --root-dir /path/to/workflow-output \
+  --function-id GO:0016597 \
+  --category GO \
+  --rank Genus \
+  --top 10 \
+  --output go_taxa.tsv
+```
+
+Omit `--category` to search all supported annotation categories. `--top`
+limits the results to the highest-support taxa per sample. Alternatively,
+provide `--gene-table` to query a particular integrated gene table, or
+`--output-dir` to select a non-default results directory.
+
+Find the most supported features associated with a taxon:
+
+```bash
+metapont query-taxon \
+  --root-dir /path/to/workflow-output \
+  --taxon Bacillus \
+  --category GO \
+  --rank Genus \
+  --top 20 \
+  --output bacillus_go.tsv
+```
+
+Taxon matching is case-insensitive and searches the chosen rank as well as the
+full lineage. `--category` is required for this query. Both query commands
+accept an explicit `--gene-table` path; plain TSV and gzip-compressed TSV files
+are supported.
+
+## Results
+
+The default output tree is:
+
+```text
+MetaPont_Results/
+├── combined/
+│   ├── all_contigs.tsv.gz
+│   └── gene_annotations.tsv.gz
+├── functional/
+│   ├── functional_abundance.tsv
+│   ├── matrices/
+│   └── taxon_function_abundance.tsv
+├── inventory/
+│   └── sample_inventory.tsv
+├── metadata/
+│   ├── input_signature.json
+│   └── run_manifest.json
+├── per_sample_contigs/
+│   └── SAMPLE_Contigs.tsv.gz
+├── summary/
+│   ├── pipeline_warnings.tsv
+│   ├── sample_inventory.tsv
+│   └── sample_summary.tsv
+└── taxonomy/
+    └── taxonomy_abundance.tsv
+```
+
+The main tables are tab-delimited; `.tsv.gz` files are gzip-compressed TSVs.
+Functional matrices are written separately for every supported annotation
+category, with both gene counts and gene read-support values. The optional
+taxon-function abundance table contains taxon/category/feature combinations
+across taxonomic ranks.
+
+Supported functional categories include `COG`, `eggNOG_OG`, `GO`, `EC`,
+`KEGG_KO`, `KEGG_Pathway`, `KEGG_Module`, `KEGG_Reaction`, `KEGG_rclass`,
+`BRITE`, `KEGG_TC`, `CAZy`, `BiGG_Reaction`, and `PFAM`.
+
+`Gene_Read_Support` is derived from read-to-CDS overlaps in the CDS summary; it
+is not a count of unique reads across genes. A read can support multiple genes
+or annotations, so functional support values are not mutually exclusive.
+Taxonomic relative abundance uses total mapped-read support as its denominator.
+
+Samples with missing or stale workflow outputs are retained where possible and
+listed in `summary/pipeline_warnings.tsv`. A clean run writes
+`MetaPont_analysis.success`; a run with warnings writes
+`completed_with_warnings.flag`.
+
+## License
+
+MetaPont is distributed under the
+[GNU General Public License v3.0 or later](LICENSE).

metapont-0.1.2/README.md

@@ -0,0 +1,202 @@
+# MetaPont v0.1.2
+
+MetaPont integrates existing metagenomic workflow outputs into per-sample and
+cross-sample tables for contigs, taxonomy, readmapping support, and eggNOG-mapper
+functional annotations. It is designed for outputs from the
+[HuwsLab Metagenomic Workflow](https://github.com/TheHuwsLab/Metagenomic_Workflow),
+but does not run assembly, readmapping, Kraken2, or eggNOG-mapper itself.
+
+## Installation
+
+MetaPont requires Python 3.10 or later and has no required third-party runtime
+dependencies.
+
+```bash
+pip install MetaPont
+```
+
+Check the installed version and available commands with:
+
+```bash
+metapont --version
+metapont --help
+```
+
+## Input layout
+
+Pass MetaPont the directory containing sample directories. Sample directories
+are selected when their names start with one of the comma-separated prefixes
+provided with `--prefix`.
+
+```text
+workflow-output/
+├── E1.0/
+│   ├── E1.0_metaspades/contigs.fasta
+│   ├── E1.0_pyrodigal/
+│   ├── E1.0_eggnog_mapper/
+│   │   └── E1.0_pyrodigal_eggnog_mapped.emapper.annotations
+│   ├── E1.0_kraken2/
+│   │   ├── E1.0_kraken2.txt
+│   │   └── E1.0_kraken2_report.txt
+│   └── E1.0_readmapped/
+│       ├── E1.0_readmapped_contig_summary.txt
+│       └── E1.0_readmapped_cds_summary.txt
+└── E2.0/
+    └── ...
+```
+
+MetaPont discovers common workflow naming variants and searches within each
+sample directory for the relevant files. The main inputs are:
+
+| Input | Used for |
+| --- | --- |
+| eggNOG-mapper `.emapper.annotations` | Gene annotations and functional features |
+| Kraken2 contig classifications and report | Contig taxonomic assignments and lineages |
+| Readmapping contig summary | Contig lengths, mapped-read counts, and mapping proportions |
+| Readmapping CDS summary | Read support attributed to annotated genes |
+| Contig FASTA | Contig inventory and lengths when a readmapping contig summary is absent |
+
+Inputs are discovered independently, so incomplete samples can still be
+included. Missing or stale outputs are reported as warnings; MetaPont does not
+rerun missing upstream analyses. Kraken2 assignments shorter than the selected
+minimum contig length are omitted from taxonomy attribution by default. This
+filter does not rerun Kraken2.
+
+## Commands
+
+### Build integrated results
+
+```bash
+metapont run \
+  --root-dir /path/to/workflow-output \
+  --prefix E
+```
+
+`--prefix` accepts comma-separated values, for example `E,L,P`. By default,
+results are written under `ROOT/MetaPont_Results`. Override that location with
+`--output-dir`.
+
+Useful options:
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--force` | Off | Regenerate outputs even when the input signature matches a cached run. |
+| `--no-heal-flags` | Off | Do not recreate missing upstream success flags when their outputs are complete and current. |
+| `--min-contig-length N` | `2500` | Minimum Kraken2-assigned contig length retained for taxonomy attribution; use `0` to disable the filter. |
+| `--taxon-function-abundance` | Off | Build the expanded taxon-by-function table. This can use substantial memory and disk space. |
+| `--plots` | Off | Write optional quick-look PNG plots. Requires the `plots` installation extra. |
+
+`metapont combine` is an alias for `metapont run`. The `metapont-combine`
+command is also available for compatibility with the earlier combine command.
+
+### Audit sample inputs
+
+```bash
+metapont inventory --root-dir /path/to/workflow-output --prefix E
+```
+
+The inventory reports discovered inputs, expected outputs, success flags, and
+warnings for each sample. Add `--heal-flags` to recreate a missing stage flag
+only when its corresponding output files are complete and current.
+
+### Summarise readmapping coverage
+
+```bash
+metapont coverage \
+  --root-dir /path/to/workflow-output \
+  --prefix E \
+  --read-length 150
+```
+
+The optional read length adds an approximate mapped-read coverage estimate.
+Without `--output`, the TSV is written to
+`MetaPont_Results/summary/contig_coverage_summary.tsv`.
+
+### Query functions and taxa
+
+Find taxa supporting a functional ID:
+
+```bash
+metapont query-function \
+  --root-dir /path/to/workflow-output \
+  --function-id GO:0016597 \
+  --category GO \
+  --rank Genus \
+  --top 10 \
+  --output go_taxa.tsv
+```
+
+Omit `--category` to search all supported annotation categories. `--top`
+limits the results to the highest-support taxa per sample. Alternatively,
+provide `--gene-table` to query a particular integrated gene table, or
+`--output-dir` to select a non-default results directory.
+
+Find the most supported features associated with a taxon:
+
+```bash
+metapont query-taxon \
+  --root-dir /path/to/workflow-output \
+  --taxon Bacillus \
+  --category GO \
+  --rank Genus \
+  --top 20 \
+  --output bacillus_go.tsv
+```
+
+Taxon matching is case-insensitive and searches the chosen rank as well as the
+full lineage. `--category` is required for this query. Both query commands
+accept an explicit `--gene-table` path; plain TSV and gzip-compressed TSV files
+are supported.
+
+## Results
+
+The default output tree is:
+
+```text
+MetaPont_Results/
+├── combined/
+│   ├── all_contigs.tsv.gz
+│   └── gene_annotations.tsv.gz
+├── functional/
+│   ├── functional_abundance.tsv
+│   ├── matrices/
+│   └── taxon_function_abundance.tsv
+├── inventory/
+│   └── sample_inventory.tsv
+├── metadata/
+│   ├── input_signature.json
+│   └── run_manifest.json
+├── per_sample_contigs/
+│   └── SAMPLE_Contigs.tsv.gz
+├── summary/
+│   ├── pipeline_warnings.tsv
+│   ├── sample_inventory.tsv
+│   └── sample_summary.tsv
+└── taxonomy/
+    └── taxonomy_abundance.tsv
+```
+
+The main tables are tab-delimited; `.tsv.gz` files are gzip-compressed TSVs.
+Functional matrices are written separately for every supported annotation
+category, with both gene counts and gene read-support values. The optional
+taxon-function abundance table contains taxon/category/feature combinations
+across taxonomic ranks.
+
+Supported functional categories include `COG`, `eggNOG_OG`, `GO`, `EC`,
+`KEGG_KO`, `KEGG_Pathway`, `KEGG_Module`, `KEGG_Reaction`, `KEGG_rclass`,
+`BRITE`, `KEGG_TC`, `CAZy`, `BiGG_Reaction`, and `PFAM`.
+
+`Gene_Read_Support` is derived from read-to-CDS overlaps in the CDS summary; it
+is not a count of unique reads across genes. A read can support multiple genes
+or annotations, so functional support values are not mutually exclusive.
+Taxonomic relative abundance uses total mapped-read support as its denominator.
+
+Samples with missing or stale workflow outputs are retained where possible and
+listed in `summary/pipeline_warnings.tsv`. A clean run writes
+`MetaPont_analysis.success`; a run with warnings writes
+`completed_with_warnings.flag`.
+
+## License
+
+MetaPont is distributed under the
+[GNU General Public License v3.0 or later](LICENSE).

{metapont-0.1.0 → metapont-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MetaPont"
-version = "0.1.0"
+version = "0.1.2"
 authors = [
     { name = "Nicholas Dimonaco", email = "nicholas@dimonaco.co.uk" }
 ]

{metapont-0.1.0 → metapont-0.1.2}/src/MetaPont/__init__.py

@@ -1,6 +1,6 @@
 """MetaPont: integrated analysis of metagenomic workflow outputs."""
 
-__version__ = "0.1.0"
+__version__ = "0.1.2"
 MetaPont_Version = f"v{__version__}"
 
 __all__ = ["__version__", "MetaPont_Version"]

{metapont-0.1.0 → metapont-0.1.2}/src/MetaPont/cli.py

@@ -94,7 +94,14 @@ def main(argv: list[str] | None = None) -> int:
     run_p.add_argument("--no-heal-flags", action="store_true", help="Do not recreate missing pipeline flags when all corresponding outputs exist.")
     run_p.add_argument("--min-contig-length", type=int, default=2500, help="Minimum contig length to retain an existing Kraken2 assignment; classifications are not rerun.")
     run_p.add_argument("--plots", action="store_true", help="Generate optional quick-look PNG plots (requires matplotlib).")
-
+    run_p.add_argument(
+        "--taxon-function-abundance",
+        action="store_true",
+        help=(
+            "Generate the expanded taxon-function abundance table. "
+            "Can require substantial memory and disk space."
+        ),
+    )
     inv_p = sub.add_parser("inventory", help="Audit per-sample inputs, pipeline outputs and success flags.")
     _add_root_prefix(inv_p)
     inv_p.add_argument("--heal-flags", action="store_true", help="Recreate missing flags only when the relevant output set is complete and current.")
@@ -105,7 +112,8 @@ def main(argv: list[str] | None = None) -> int:
     cov_p.add_argument("--output", default=None, help="Output TSV path (defaults under MetaPont_Results/summary).")
 
     qf_p = sub.add_parser("query-function", help="Find taxa supporting a particular eggNOG functional ID.")
-    qf_p.add_argument("--root-dir", "-d", required=True)
+    qf_p.add_argument("--root-dir", "-d", default=None,
+                      help="Workflow root used to find the default gene table; not needed with --gene-table or --output-dir.")
     qf_p.add_argument("--output-dir", default=None)
     qf_p.add_argument("--gene-table", default=None, help="Gene annotation TSV/TSV.GZ; defaults to the integrated output table.")
     qf_p.add_argument("--function-id", "-f", required=True, help="Exact function ID, e.g. GO:0016597 or EC:2.7.11.1.")
@@ -132,6 +140,7 @@ def main(argv: list[str] | None = None) -> int:
                 min_contig_length=args.min_contig_length,
                 heal_flags=not args.no_heal_flags,
                 force=args.force,
+                include_taxon_function_abundance=args.taxon_function_abundance,
             )
             if args.plots:
                 output_root = Path(result["output_dir"])

{metapont-0.1.0 → metapont-0.1.2}/src/MetaPont/pipeline.py

@@ -201,7 +201,7 @@ def _iter_base_contigs(sample: SamplePaths, assignments: dict[str, dict[str, Any
             }
 
 
-def _annotation_maps(sample: SamplePaths, contig_ids: set[str], assignments: dict[str, dict[str, Any]], gene_support: dict[str, int], gene_writer: csv.DictWriter):
+def _annotation_maps(sample: SamplePaths, contig_ids: set[str], assignments: dict[str, dict[str, Any]], gene_support: dict[str, int], gene_writer: csv.DictWriter, include_taxon_functions: bool = False):
     by_contig: dict[str, dict[str, Any]] = {}
     gene_count = 0
     functional: dict[tuple[str, str], list[int]] = defaultdict(lambda: [0, 0])
@@ -233,13 +233,14 @@ def _annotation_maps(sample: SamplePaths, contig_ids: set[str], assignments: dic
                 record["features"][category].add(feature)
                 functional[(category, feature)][0] += 1
                 functional[(category, feature)][1] += support
-                lineage = assignments.get(contig, {}).get("lineage", empty_lineage())
-                for rank in LINEAGE_RANKS:
-                    taxon = _lineage_taxon(lineage, rank)
-                    if taxon != UNKNOWN:
-                        lineage_value = lineage_string(lineage)
-                        taxon_function[(rank, taxon, lineage_value, f"{category}\t{feature}")][0] += 1
-                        taxon_function[(rank, taxon, lineage_value, f"{category}\t{feature}")][1] += support
+                if include_taxon_functions:
+                    lineage = assignments.get(contig, {}).get("lineage", empty_lineage())
+                    for rank in LINEAGE_RANKS:
+                        taxon = _lineage_taxon(lineage, rank)
+                        if taxon != UNKNOWN:
+                            lineage_value = lineage_string(lineage)
+                            taxon_function[(rank, taxon, lineage_value, f"{category}\t{feature}")][0] += 1
+                            taxon_function[(rank, taxon, lineage_value, f"{category}\t{feature}")][1] += support
         tax = assignments.get(contig, {})
         gene_count += 1
         gene_lineage = tax.get("lineage", empty_lineage())
@@ -284,7 +285,8 @@ def _contig_row(sample_name: str, base: dict[str, Any], tax: dict[str, Any] | No
     return out
 
 
-def _input_signature(samples: list[SamplePaths], min_contig_length: int) -> dict[str, Any]:
+def _input_signature(samples: list[SamplePaths], min_contig_length: int,
+                    include_taxon_function_abundance: bool) -> dict[str, Any]:
     records = []
     for sample in samples:
         selected = [
@@ -296,13 +298,17 @@ def _input_signature(samples: list[SamplePaths], min_contig_length: int) -> dict
             if path and path.is_file():
                 st = path.stat()
                 records.append({"sample": sample.name, "path": str(path), "size": st.st_size, "mtime_ns": st.st_mtime_ns})
-    parameters = {"min_contig_length": int(min_contig_length)}
+    parameters = {
+        "min_contig_length": int(min_contig_length),
+        "include_taxon_function_abundance": include_taxon_function_abundance,
+    }
     payload = {"inputs": records, "parameters": parameters}
     digest = hashlib.sha256(json.dumps(payload, sort_keys=True).encode()).hexdigest()
     return {"version": __version__, "signature": digest, "parameters": parameters, "inputs": records}
 
 
-def _valid_cached_outputs(output_root: Path, signature: dict[str, Any], force: bool, samples: list[SamplePaths]) -> bool:
+def _valid_cached_outputs(output_root: Path, signature: dict[str, Any], force: bool,
+                          samples: list[SamplePaths], include_taxon_function_abundance: bool) -> bool:
     manifest = output_root / "metadata" / "input_signature.json"
     required = [
         output_root / "combined" / "all_contigs.tsv.gz",
@@ -311,10 +317,13 @@ def _valid_cached_outputs(output_root: Path, signature: dict[str, Any], force: b
         output_root / "summary" / "sample_inventory.tsv",
         output_root / "taxonomy" / "taxonomy_abundance.tsv",
         output_root / "functional" / "functional_abundance.tsv",
-        output_root / "functional" / "taxon_function_abundance.tsv",
         output_root / "summary" / "pipeline_warnings.tsv",
         output_root / "metadata" / "run_manifest.json",
     ]
+    if include_taxon_function_abundance:
+        required.append(
+            output_root / "functional" / "taxon_function_abundance.tsv"
+        )
     required.extend(output_root / "per_sample_contigs" / f"{sample.name}_Contigs.tsv.gz" for sample in samples)
     for category in FEATURE_COLUMNS:
         required.append(output_root / "functional" / "matrices" / f"{category}_gene_counts.tsv")
@@ -329,7 +338,7 @@ def _valid_cached_outputs(output_root: Path, signature: dict[str, Any], force: b
 
 
 def run_analysis(root_dir: str | Path, prefixes: str, output_dir: str | Path | None = None,
-                 min_contig_length: int = 2500, heal_flags: bool = True, force: bool = False) -> dict[str, Any]:
+                 min_contig_length: int = 2500, heal_flags: bool = True, force: bool = False, include_taxon_function_abundance: bool = True) -> dict[str, Any]:
     """Build the integrated MetaPont result set; partial samples are included with warnings."""
     root = Path(root_dir).expanduser().resolve()
     output_root = Path(output_dir).expanduser().resolve() if output_dir else root / OUTPUT_DIRNAME
@@ -350,8 +359,8 @@ def run_analysis(root_dir: str | Path, prefixes: str, output_dir: str | Path | N
         with (dirs["inventory"] / "flag_healing.log").open("a", encoding="utf-8") as handle:
             handle.write("\n".join(healed_events) + "\n")
 
-    signature = _input_signature(samples, min_contig_length)
-    if _valid_cached_outputs(output_root, signature, force, samples):
+    signature = _input_signature(samples, min_contig_length, include_taxon_function_abundance)
+    if _valid_cached_outputs(output_root, signature, force, samples, include_taxon_function_abundance):
         warnings_path = dirs["summary"] / "pipeline_warnings.tsv"
         has_warnings = _nonempty(warnings_path) and sum(1 for _ in warnings_path.open(encoding="utf-8")) > 1
         complete_flag = output_root / "MetaPont_analysis.success"
@@ -410,7 +419,8 @@ def run_analysis(root_dir: str | Path, prefixes: str, output_dir: str | Path | N
             gene_support = parse_cds_summary(sample.cds_summary)
             known_contigs = set(assignments)
             annotation_map, gene_count, sample_functional, sample_taxon_functions = _annotation_maps(
-                sample, known_contigs, assignments, gene_support, gene_writer
+                sample, known_contigs, assignments, gene_support, gene_writer, include_taxon_functions=include_taxon_function_abundance,
+
             )
             for (category, feature), counts in sample_functional.items():
                 functional[(category, feature)][0] += counts[0]