moducomp 0.7.11__tar.gz → 0.7.13__tar.gz

{moducomp-0.7.11 → moducomp-0.7.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moducomp
-Version: 0.7.11
+Version: 0.7.13
 Summary: moducomp: metabolic module completeness and complementarity for microbiomes.
 Keywords: bioinformatics,microbiome,metabolic,kegg,genomics
 Author-email: "Juan C. Villada" <jvillada@lbl.gov>
@@ -38,6 +38,7 @@ Project-URL: Repository, https://github.com/NeLLi-team/moducomp
 - Tracks and reports the actual proteins that are responsible for the completion of the module in the combination of N genomes.
 - **Automatic resource monitoring** with timestamped logs tracking CPU usage, memory consumption, and runtime for reproducibility.
 - **Consistent logging to stdout/stderr** with a per-command resource summary emitted at the end of each run.
+- **Built-in validation (`moducomp validate`)** for scientific consistency checks across annotations, KO matrices, KPCT outputs, and complementarity reports.
 
 ## Installation (Recommended)
 
@@ -59,16 +60,16 @@ pixi global install \
 
 ## Setup data (required)
 
-`moducomp` needs the eggNOG-mapper database to run. Download it once:
+`moducomp` needs the eggNOG-mapper database to run. The primary (recommended) way to download it is using the `download_eggnog_data.py` wrapper, which mirrors the upstream downloader behavior. For upstream details, see the eggNOG-mapper setup guide: [eggNOG-mapper database setup](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.13#user-content-Setup).
 
 ```bash
 export EGGNOG_DATA_DIR="/path/to/eggnog-data"
-moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
-# or the standalone script:
-# download_eggnog_data.py
+download_eggnog_data.py --eggnog-data-dir "$EGGNOG_DATA_DIR"
+# equivalent:
+# moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
 ```
 
-If `EGGNOG_DATA_DIR` is not set, `moducomp download-eggnog-data` defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
+If `EGGNOG_DATA_DIR` is not set, the downloader defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
 
 ### Quick test
 
@@ -148,6 +149,9 @@ This section lists all CLI options implemented today, along with their default v
 | `--del-tmp/--keep-tmp` | `true` | Delete temporary files after completion. |
 | `--lowmem/--fullmem` (`--low-mem/--full-mem`) | `fullmem` | Run eggNOG-mapper without `--dbmem` to reduce RAM. |
 | `--verbose/--quiet` | `false` | Enable verbose progress output. |
+| `--validate/--no-validate` | `validate` | Run post-run validation checks. |
+| `--validate-report/--no-validate-report` | `validate-report` | Write `validation_report.json` in the output directory. |
+| `--validate-strict/--validate-lenient` | `lenient` | Treat validation warnings as failures when strict. |
 | `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
 | `--eggnog-data-dir` | `EGGNOG_DATA_DIR` | Path to eggNOG-mapper data (sets `EGGNOG_DATA_DIR`). |
 
@@ -162,6 +166,9 @@ This section lists all CLI options implemented today, along with their default v
 | `--del-tmp/--keep-tmp` | `true` | Delete temporary files after the test completes. |
 | `--lowmem/--fullmem` (`--low-mem/--full-mem`) | `lowmem` | Low-memory mode is the default for tests. |
 | `--verbose/--quiet` | `verbose` | Verbose output is the default for tests. |
+| `--validate/--no-validate` | `validate` | Run post-run validation checks. |
+| `--validate-report/--no-validate-report` | `validate-report` | Write `validation_report.json` in the output directory. |
+| `--validate-strict/--validate-lenient` | `lenient` | Treat validation warnings as failures when strict. |
 | `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
 | `--eggnog-data-dir` | `EGGNOG_DATA_DIR` | Path to eggNOG-mapper data (sets `EGGNOG_DATA_DIR`). |
 
@@ -174,6 +181,21 @@ This section lists all CLI options implemented today, along with their default v
 | `--del-tmp/--keep-tmp` | `true` | Delete temporary files after completion. |
 | `--ncpus`, `-n` | `16` | CPU cores for KPCT parallel processing. |
 | `--verbose/--quiet` | `false` | Enable verbose progress output. |
+| `--validate/--no-validate` | `validate` | Run post-run validation checks. |
+| `--validate-report/--no-validate-report` | `validate-report` | Write `validation_report.json` in the output directory. |
+| `--validate-strict/--validate-lenient` | `lenient` | Treat validation warnings as failures when strict. |
+| `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
+
+#### `validate` command (positional args: `savedir`)
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--mode` | `auto` | Validation mode: `auto`, `pipeline`, or `ko-matrix`. |
+| `--calculate-complementarity`, `-c` | `auto-detect` | Expected complementarity size (0 disables). |
+| `--kpct-outprefix` | `output_give_completeness` | KPCT output prefix used during analysis. |
+| `--strict/--lenient` | `lenient` | Treat warnings as failures when strict. |
+| `--report` | _none_ | Write JSON validation report to this path. |
+| `--verbose/--quiet` | `false` | Enable verbose progress output. |
 | `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
 
 #### `download-eggnog-data` command
@@ -198,6 +220,33 @@ This section lists all CLI options implemented today, along with their default v
 - For KPCT parallel processing, the system creates the same number of chunks as CPU cores specified
 - Example: `--ncpus 8` will use 8 cores and create 8 chunks for optimal parallel processing
 
+### Validation (QC)
+
+Use the built-in validator to check scientific consistency across outputs after a run. The validator compares:
+- KO sets and counts between eggNOG-mapper annotations and `kos_matrix.csv`
+- KO sets between `kos_matrix.csv` and `ko_file_for_kpct.txt`
+- KPCT contigs vs pathways outputs
+- Module completeness ranges and combination naming
+- Complementarity reports versus module completeness values
+- Protein provenance fields (pipeline mode) or placeholders (KO-matrix mode)
+
+Example:
+
+```bash
+# Validation runs by default after pipeline/analyze/test.
+# Use --no-validate to disable or --no-validate-report to skip JSON output.
+# When validation reports errors (or warnings in strict mode), the command exits non-zero.
+
+# Validate a pipeline run and write a JSON report
+moducomp validate /path/to/output --mode pipeline --report /path/to/output/validation_report.json
+
+# Validate KO-matrix mode outputs (non-default KPCT prefix)
+moducomp validate /path/to/output --mode ko-matrix --kpct-outprefix my_prefix
+
+# Treat warnings as failures
+moducomp validate /path/to/output --strict
+```
+
 ### ⚠️ Important note 1
 
 **Prepare FAA files**: Ensure FAA headers are in the form `>genomeName|proteinId`, or use the `--adapt-headers` option to format your headers into `>fileName_prefix|protein_id_counter`.
@@ -211,7 +260,7 @@ This section lists all CLI options implemented today, along with their default v
 You can override the bundled data location with `MODUCOMP_DATA_DIR`.
 When working from source, the bundled test genomes live at `moducomp/data/test_genomes`.
 
-`download_eggnog_data.py` is provided by eggnog-mapper and is available in the Pixi environment (or via `pixi global` installs).
+`download_eggnog_data.py` is exposed by `moducomp` as a convenience wrapper for the eggnog-mapper downloader and is available in the Pixi environment (including `pixi global` installs).
 
 Pixi task (supports passing a custom location):
 
@@ -298,15 +347,38 @@ moducomp analyze-ko-matrix ./ko_matrix.csv ./output_moderate --ncpus 16 --calcul
 moducomp pipeline ./genomes ./output_lowmem --ncpus 8 --lowmem --calculate-complementarity 2
 ```
 
-## Output files
+## Expected outputs
+
+The sections below describe the expected output files, naming conventions, and the column-level meaning of each file. These details are the same for `moducomp pipeline` and `moducomp test` (pipeline mode), and the subset noted for `moducomp analyze-ko-matrix` (KO-matrix mode).
+
+**Naming conventions**
+
+Genome identifiers are stored as `taxon_oid`. In pipeline mode, ModuComp expects protein headers in the format `genome_id|protein_id`. If you set `--adapt-headers`, ModuComp rewrites headers to `>genomeName|protein_N`, where `genomeName` is the FAA filename stem. Combination identifiers use `__` (double underscore), for example `GenomeA__GenomeB`, and `n_members` in `module_completeness.tsv` records the size of each combination.
+
+**Pipeline mode outputs (`moducomp pipeline`, `moducomp test`)**
+
+- `emapper_out.emapper.annotations`: Full eggNOG-mapper annotations. The `#query` column must match `genome_id|protein_id`. `KEGG_ko` entries are prefixed `ko:KXXXXX` and are converted to `KXXXXX` for downstream matrices.
+- `kos_matrix.csv`: Genome × KO count matrix. Columns: `taxon_oid` followed by KO IDs (e.g., `K00001`). Values are integer protein counts per KO.
+- `ko_file_for_kpct.txt`: KPCT input file. Each line starts with `taxon_oid` followed by the set of KO IDs present in that genome or combination. If `--calculate-complementarity` is `N>=2`, combinations up to `N` are included as `GenomeA__GenomeB`.
+- `output_give_completeness_contigs.with_weights.tsv`: KPCT module results per genome/combination. Columns: `contig` (genome/combination ID), `module_accession`, `completeness` (0–100), `pathway_name`, `pathway_class`, `matching_ko` (KO weights), `missing_ko`.
+- `output_give_completeness_pathways.with_weights.tsv`: Same rows and order as the contigs file, but without the `contig` column. This is provided for compatibility with legacy tools; prefer the contigs file when you need genome-level provenance.
+- `module_completeness.tsv`: Pivoted module completeness matrix. Columns: `n_members`, `taxon_oid`, followed by KEGG module IDs (`M00001`, …). Values are numeric percentages in the range 0–100.
+- `module_completeness_complementarity_Nmember.tsv`: Complementarity report for `N`-member combinations (only when `--calculate-complementarity N` is set). Columns: `taxon_oid_1..N`, `completeness_taxon_oid_1..N`, `module_id`, `module_name`, `pathway_class`, `matching_ko`, `proteins_taxon_oid_1..N`. Protein fields list contributing proteins per KO (from eggNOG-mapper) as `{'KXXXXX': 'genome|protein'}`.
+- `logs/moducomp.log`: Detailed run log with structured progress messages and per-command resource summaries.
+- `logs/resource_usage_YYYYMMDD_HHMMSS.log`: Resource monitoring log capturing wall time, CPU time, CPU utilization, peak RAM, and exit code for each monitored command.
+- `tmp/` (only if `--keep-tmp`): Intermediate files such as `merged_genomes.faa`, `emapper_output/`, and KPCT chunk outputs.
+- `validation_report.json` (default when validation is enabled): JSON report produced by the validator.
 
-`moducomp` generates several output files in the specified output directory:
+**KO-matrix mode outputs (`moducomp analyze-ko-matrix`)**
 
-- **`kos_matrix.csv`**: Matrix of KO counts for each genome
-- **`module_completeness.tsv`**: Module completeness scores for individual genomes and combinations
-- **`module_completeness_complementarity_Nmember.tsv`**: Complementarity reports (if requested)
-- **`logs/resource_usage_YYYYMMDD_HHMMSS.log`**: Resource monitoring log with CPU, memory, and runtime metrics for reproducibility
-- **`logs/moducomp.log`**: Detailed pipeline execution log with a per-command resource summary at the end of the run
+- `kos_matrix.csv`: A copy of the input KO matrix (same format as above).
+- `ko_file_for_kpct.txt`: KPCT input generated from the KO matrix. If `--calculate-complementarity` is set, combination lines are added using `GenomeA__GenomeB` identifiers.
+- `output_give_completeness_contigs.with_weights.tsv`: KPCT module results per genome/combination (same format as pipeline mode).
+- `output_give_completeness_pathways.with_weights.tsv`: Same rows as the contigs file, without the `contig` column.
+- `module_completeness.tsv`: Module completeness matrix (same format as pipeline mode).
+- `module_completeness_complementarity_Nmember.tsv`: Complementarity report. Protein contribution columns are filled with `No protein data available for <genome>` because no eggNOG-mapper annotations are available in KO-matrix mode.
+- `logs/moducomp.log` and `logs/resource_usage_YYYYMMDD_HHMMSS.log`: Standard run logs and resource summaries.
+- `validation_report.json` (default when validation is enabled): JSON report produced by the validator.
 
 ## Citation
 Villada, JC. & Schulz, F. (2025). Assessment of metabolic module completeness of genomes and metabolic complementarity in microbiomes with `moducomp` . `moducomp` (v0.5.1) Zenodo. https://doi.org/10.5281/zenodo.16116092

{moducomp-0.7.11 → moducomp-0.7.13}/README.md

@@ -13,6 +13,7 @@
 - Tracks and reports the actual proteins that are responsible for the completion of the module in the combination of N genomes.
 - **Automatic resource monitoring** with timestamped logs tracking CPU usage, memory consumption, and runtime for reproducibility.
 - **Consistent logging to stdout/stderr** with a per-command resource summary emitted at the end of each run.
+- **Built-in validation (`moducomp validate`)** for scientific consistency checks across annotations, KO matrices, KPCT outputs, and complementarity reports.
 
 ## Installation (Recommended)
 
@@ -34,16 +35,16 @@ pixi global install \
 
 ## Setup data (required)
 
-`moducomp` needs the eggNOG-mapper database to run. Download it once:
+`moducomp` needs the eggNOG-mapper database to run. The primary (recommended) way to download it is using the `download_eggnog_data.py` wrapper, which mirrors the upstream downloader behavior. For upstream details, see the eggNOG-mapper setup guide: [eggNOG-mapper database setup](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.13#user-content-Setup).
 
 ```bash
 export EGGNOG_DATA_DIR="/path/to/eggnog-data"
-moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
-# or the standalone script:
-# download_eggnog_data.py
+download_eggnog_data.py --eggnog-data-dir "$EGGNOG_DATA_DIR"
+# equivalent:
+# moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
 ```
 
-If `EGGNOG_DATA_DIR` is not set, `moducomp download-eggnog-data` defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
+If `EGGNOG_DATA_DIR` is not set, the downloader defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
 
 ### Quick test
 
@@ -123,6 +124,9 @@ This section lists all CLI options implemented today, along with their default v
 | `--del-tmp/--keep-tmp` | `true` | Delete temporary files after completion. |
 | `--lowmem/--fullmem` (`--low-mem/--full-mem`) | `fullmem` | Run eggNOG-mapper without `--dbmem` to reduce RAM. |
 | `--verbose/--quiet` | `false` | Enable verbose progress output. |
+| `--validate/--no-validate` | `validate` | Run post-run validation checks. |
+| `--validate-report/--no-validate-report` | `validate-report` | Write `validation_report.json` in the output directory. |
+| `--validate-strict/--validate-lenient` | `lenient` | Treat validation warnings as failures when strict. |
 | `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
 | `--eggnog-data-dir` | `EGGNOG_DATA_DIR` | Path to eggNOG-mapper data (sets `EGGNOG_DATA_DIR`). |
 
@@ -137,6 +141,9 @@ This section lists all CLI options implemented today, along with their default v
 | `--del-tmp/--keep-tmp` | `true` | Delete temporary files after the test completes. |
 | `--lowmem/--fullmem` (`--low-mem/--full-mem`) | `lowmem` | Low-memory mode is the default for tests. |
 | `--verbose/--quiet` | `verbose` | Verbose output is the default for tests. |
+| `--validate/--no-validate` | `validate` | Run post-run validation checks. |
+| `--validate-report/--no-validate-report` | `validate-report` | Write `validation_report.json` in the output directory. |
+| `--validate-strict/--validate-lenient` | `lenient` | Treat validation warnings as failures when strict. |
 | `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
 | `--eggnog-data-dir` | `EGGNOG_DATA_DIR` | Path to eggNOG-mapper data (sets `EGGNOG_DATA_DIR`). |
 
@@ -149,6 +156,21 @@ This section lists all CLI options implemented today, along with their default v
 | `--del-tmp/--keep-tmp` | `true` | Delete temporary files after completion. |
 | `--ncpus`, `-n` | `16` | CPU cores for KPCT parallel processing. |
 | `--verbose/--quiet` | `false` | Enable verbose progress output. |
+| `--validate/--no-validate` | `validate` | Run post-run validation checks. |
+| `--validate-report/--no-validate-report` | `validate-report` | Write `validation_report.json` in the output directory. |
+| `--validate-strict/--validate-lenient` | `lenient` | Treat validation warnings as failures when strict. |
+| `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
+
+#### `validate` command (positional args: `savedir`)
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--mode` | `auto` | Validation mode: `auto`, `pipeline`, or `ko-matrix`. |
+| `--calculate-complementarity`, `-c` | `auto-detect` | Expected complementarity size (0 disables). |
+| `--kpct-outprefix` | `output_give_completeness` | KPCT output prefix used during analysis. |
+| `--strict/--lenient` | `lenient` | Treat warnings as failures when strict. |
+| `--report` | _none_ | Write JSON validation report to this path. |
+| `--verbose/--quiet` | `false` | Enable verbose progress output. |
 | `--log-level`, `-l` | `INFO` | Logging level: `DEBUG`, `INFO`, `WARNING`, `ERROR`. |
 
 #### `download-eggnog-data` command
@@ -173,6 +195,33 @@ This section lists all CLI options implemented today, along with their default v
 - For KPCT parallel processing, the system creates the same number of chunks as CPU cores specified
 - Example: `--ncpus 8` will use 8 cores and create 8 chunks for optimal parallel processing
 
+### Validation (QC)
+
+Use the built-in validator to check scientific consistency across outputs after a run. The validator compares:
+- KO sets and counts between eggNOG-mapper annotations and `kos_matrix.csv`
+- KO sets between `kos_matrix.csv` and `ko_file_for_kpct.txt`
+- KPCT contigs vs pathways outputs
+- Module completeness ranges and combination naming
+- Complementarity reports versus module completeness values
+- Protein provenance fields (pipeline mode) or placeholders (KO-matrix mode)
+
+Example:
+
+```bash
+# Validation runs by default after pipeline/analyze/test.
+# Use --no-validate to disable or --no-validate-report to skip JSON output.
+# When validation reports errors (or warnings in strict mode), the command exits non-zero.
+
+# Validate a pipeline run and write a JSON report
+moducomp validate /path/to/output --mode pipeline --report /path/to/output/validation_report.json
+
+# Validate KO-matrix mode outputs (non-default KPCT prefix)
+moducomp validate /path/to/output --mode ko-matrix --kpct-outprefix my_prefix
+
+# Treat warnings as failures
+moducomp validate /path/to/output --strict
+```
+
 ### ⚠️ Important note 1
 
 **Prepare FAA files**: Ensure FAA headers are in the form `>genomeName|proteinId`, or use the `--adapt-headers` option to format your headers into `>fileName_prefix|protein_id_counter`.
@@ -186,7 +235,7 @@ This section lists all CLI options implemented today, along with their default v
 You can override the bundled data location with `MODUCOMP_DATA_DIR`.
 When working from source, the bundled test genomes live at `moducomp/data/test_genomes`.
 
-`download_eggnog_data.py` is provided by eggnog-mapper and is available in the Pixi environment (or via `pixi global` installs).
+`download_eggnog_data.py` is exposed by `moducomp` as a convenience wrapper for the eggnog-mapper downloader and is available in the Pixi environment (including `pixi global` installs).
 
 Pixi task (supports passing a custom location):
 
@@ -273,15 +322,38 @@ moducomp analyze-ko-matrix ./ko_matrix.csv ./output_moderate --ncpus 16 --calcul
 moducomp pipeline ./genomes ./output_lowmem --ncpus 8 --lowmem --calculate-complementarity 2
 ```
 
-## Output files
+## Expected outputs
+
+The sections below describe the expected output files, naming conventions, and the column-level meaning of each file. These details are the same for `moducomp pipeline` and `moducomp test` (pipeline mode), and the subset noted for `moducomp analyze-ko-matrix` (KO-matrix mode).
+
+**Naming conventions**
+
+Genome identifiers are stored as `taxon_oid`. In pipeline mode, ModuComp expects protein headers in the format `genome_id|protein_id`. If you set `--adapt-headers`, ModuComp rewrites headers to `>genomeName|protein_N`, where `genomeName` is the FAA filename stem. Combination identifiers use `__` (double underscore), for example `GenomeA__GenomeB`, and `n_members` in `module_completeness.tsv` records the size of each combination.
+
+**Pipeline mode outputs (`moducomp pipeline`, `moducomp test`)**
+
+- `emapper_out.emapper.annotations`: Full eggNOG-mapper annotations. The `#query` column must match `genome_id|protein_id`. `KEGG_ko` entries are prefixed `ko:KXXXXX` and are converted to `KXXXXX` for downstream matrices.
+- `kos_matrix.csv`: Genome × KO count matrix. Columns: `taxon_oid` followed by KO IDs (e.g., `K00001`). Values are integer protein counts per KO.
+- `ko_file_for_kpct.txt`: KPCT input file. Each line starts with `taxon_oid` followed by the set of KO IDs present in that genome or combination. If `--calculate-complementarity` is `N>=2`, combinations up to `N` are included as `GenomeA__GenomeB`.
+- `output_give_completeness_contigs.with_weights.tsv`: KPCT module results per genome/combination. Columns: `contig` (genome/combination ID), `module_accession`, `completeness` (0–100), `pathway_name`, `pathway_class`, `matching_ko` (KO weights), `missing_ko`.
+- `output_give_completeness_pathways.with_weights.tsv`: Same rows and order as the contigs file, but without the `contig` column. This is provided for compatibility with legacy tools; prefer the contigs file when you need genome-level provenance.
+- `module_completeness.tsv`: Pivoted module completeness matrix. Columns: `n_members`, `taxon_oid`, followed by KEGG module IDs (`M00001`, …). Values are numeric percentages in the range 0–100.
+- `module_completeness_complementarity_Nmember.tsv`: Complementarity report for `N`-member combinations (only when `--calculate-complementarity N` is set). Columns: `taxon_oid_1..N`, `completeness_taxon_oid_1..N`, `module_id`, `module_name`, `pathway_class`, `matching_ko`, `proteins_taxon_oid_1..N`. Protein fields list contributing proteins per KO (from eggNOG-mapper) as `{'KXXXXX': 'genome|protein'}`.
+- `logs/moducomp.log`: Detailed run log with structured progress messages and per-command resource summaries.
+- `logs/resource_usage_YYYYMMDD_HHMMSS.log`: Resource monitoring log capturing wall time, CPU time, CPU utilization, peak RAM, and exit code for each monitored command.
+- `tmp/` (only if `--keep-tmp`): Intermediate files such as `merged_genomes.faa`, `emapper_output/`, and KPCT chunk outputs.
+- `validation_report.json` (default when validation is enabled): JSON report produced by the validator.
 
-`moducomp` generates several output files in the specified output directory:
+**KO-matrix mode outputs (`moducomp analyze-ko-matrix`)**
 
-- **`kos_matrix.csv`**: Matrix of KO counts for each genome
-- **`module_completeness.tsv`**: Module completeness scores for individual genomes and combinations
-- **`module_completeness_complementarity_Nmember.tsv`**: Complementarity reports (if requested)
-- **`logs/resource_usage_YYYYMMDD_HHMMSS.log`**: Resource monitoring log with CPU, memory, and runtime metrics for reproducibility
-- **`logs/moducomp.log`**: Detailed pipeline execution log with a per-command resource summary at the end of the run
+- `kos_matrix.csv`: A copy of the input KO matrix (same format as above).
+- `ko_file_for_kpct.txt`: KPCT input generated from the KO matrix. If `--calculate-complementarity` is set, combination lines are added using `GenomeA__GenomeB` identifiers.
+- `output_give_completeness_contigs.with_weights.tsv`: KPCT module results per genome/combination (same format as pipeline mode).
+- `output_give_completeness_pathways.with_weights.tsv`: Same rows as the contigs file, without the `contig` column.
+- `module_completeness.tsv`: Module completeness matrix (same format as pipeline mode).
+- `module_completeness_complementarity_Nmember.tsv`: Complementarity report. Protein contribution columns are filled with `No protein data available for <genome>` because no eggNOG-mapper annotations are available in KO-matrix mode.
+- `logs/moducomp.log` and `logs/resource_usage_YYYYMMDD_HHMMSS.log`: Standard run logs and resource summaries.
+- `validation_report.json` (default when validation is enabled): JSON report produced by the validator.
 
 ## Citation
 Villada, JC. & Schulz, F. (2025). Assessment of metabolic module completeness of genomes and metabolic complementarity in microbiomes with `moducomp` . `moducomp` (v0.5.1) Zenodo. https://doi.org/10.5281/zenodo.16116092

{moducomp-0.7.11 → moducomp-0.7.13}/moducomp/__init__.py

@@ -2,7 +2,7 @@
 moducomp: metabolic module completeness and complementarity for microbiomes.
 """
 
-__version__ = "0.7.11"
+__version__ = "0.7.13"
 __author__ = "Juan C. Villada"
 __email__ = "jvillada@lbl.gov"
 __title__ = "moducomp"