moducomp 0.7.8__tar.gz → 0.7.9__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {moducomp-0.7.8 → moducomp-0.7.9}/PKG-INFO +5 -3
- {moducomp-0.7.8 → moducomp-0.7.9}/README.md +4 -2
- {moducomp-0.7.8 → moducomp-0.7.9}/moducomp/__init__.py +1 -1
- {moducomp-0.7.8 → moducomp-0.7.9}/moducomp/moducomp.py +432 -269
- {moducomp-0.7.8 → moducomp-0.7.9}/recipe.yaml +2 -2
- {moducomp-0.7.8 → moducomp-0.7.9}/.gitignore +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/LICENSE.txt +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/moducomp/__main__.py +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/moducomp/data/test_genomes/IMG2562617132.faa +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/moducomp/data/test_genomes/IMG2568526683.faa +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/moducomp/data/test_genomes/IMG2740892217.faa +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/pixi.lock +0 -0
- {moducomp-0.7.8 → moducomp-0.7.9}/pyproject.toml +0 -0
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Metadata-Version: 2.4
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Name: moducomp
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Version: 0.7.
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Version: 0.7.9
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Summary: moducomp: metabolic module completeness and complementarity for microbiomes.
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Keywords: bioinformatics,microbiome,metabolic,kegg,genomics
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Author-email: "Juan C. Villada" <jvillada@lbl.gov>
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moducomp test --ncpus 16 --calculate-complementarity 2 --eggnog-data-dir "$EGGNOG_DATA_DIR"
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```
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The test command runs in low-memory mode by default. If you have plenty of RAM and want full-memory mode, add `--fullmem` (or `--full-mem`).
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### Developer install (Pixi)
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If you want to download the code and develop locally:
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### ⚠️ Important note 2
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`moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` when running the `pipeline` command**.
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`moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` (`--low-mem`) when running the `pipeline` command**. The `test` command uses low-memory mode by default and can be switched to full memory with `--fullmem` (`--full-mem`).
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### Notes on bundled test data
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--ncpus <number_of_cpus_to_use> \
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--calculate-complementarity <N> # 0 to disable, 2 for 2-member, 3 for 3-member complementarity.
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# Optional flags:
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# --lowmem
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# --lowmem/--fullmem # Optional: Use low-mem if you have less than 64GB of RAM (default is full mem)
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# --adapt-headers # If your FASTA headers need modification
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# --del-tmp # To delete temporary files
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# --eggnog-data-dir /path # If EGGNOG_DATA_DIR is not set
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moducomp test --ncpus 16 --calculate-complementarity 2 --eggnog-data-dir "$EGGNOG_DATA_DIR"
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```
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The test command runs in low-memory mode by default. If you have plenty of RAM and want full-memory mode, add `--fullmem` (or `--full-mem`).
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### Developer install (Pixi)
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If you want to download the code and develop locally:
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### ⚠️ Important note 2
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`moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` when running the `pipeline` command**.
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`moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` (`--low-mem`) when running the `pipeline` command**. The `test` command uses low-memory mode by default and can be switched to full memory with `--fullmem` (`--full-mem`).
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### Notes on bundled test data
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--ncpus <number_of_cpus_to_use> \
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--calculate-complementarity <N> # 0 to disable, 2 for 2-member, 3 for 3-member complementarity.
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# Optional flags:
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# --lowmem
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# --lowmem/--fullmem # Optional: Use low-mem if you have less than 64GB of RAM (default is full mem)
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# --adapt-headers # If your FASTA headers need modification
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# --del-tmp # To delete temporary files
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# --eggnog-data-dir /path # If EGGNOG_DATA_DIR is not set
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