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, 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.

pip install MetaPont

Check the installed version and available commands with:

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.

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:

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

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:

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

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

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:

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:

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:

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.