MetaPont 0.1.1__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-0.1.1 → metapont-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MetaPont"
-version = "0.1.1"
+version = "0.1.2"
 authors = [
     { name = "Nicholas Dimonaco", email = "nicholas@dimonaco.co.uk" }
 ]

{metapont-0.1.1 → metapont-0.1.2}/src/MetaPont/__init__.py

@@ -1,6 +1,6 @@
 """MetaPont: integrated analysis of metagenomic workflow outputs."""
 
-__version__ = "0.1.1"
+__version__ = "0.1.2"
 MetaPont_Version = f"v{__version__}"
 
 __all__ = ["__version__", "MetaPont_Version"]

{metapont-0.1.1 → metapont-0.1.2}/src/MetaPont/pipeline.py

@@ -285,7 +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 = [
@@ -306,7 +307,8 @@ def _input_signature(samples: list[SamplePaths], min_contig_length: int) -> dict
     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",
@@ -357,8 +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"

metapont-0.1.2/src/MetaPont.egg-info/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).