[](https://gitpod.io/#https://github.com/rpetit3/sizemeup)
# `sizemeup`
`sizemeup` is a simple tool to retrieve the genome size for a given species name or tax ID. It utilizes
known genome sizes available from [NCBI's Assembly Reports](https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_species_genome_size.txt)
in combination with user provided genome sizes that may not be available from NCBI.
## Contributing
If you have a species of interest that is not available in the NCBI Assembly Reports, please
consider submitting an issue so that we can get it added to `sizemeup`. Otherwise, if you have
ideas to improve `sizemeup` please feel free to!
## Installation
You can install `sizemeup` using `conda`:
```bash
conda create -n sizemeup -c conda-forge -c bioconda sizemeup
conda activate sizemeup
sizemeup --help
```
## Available Commands
### `sizemeup`
`sizemeup` is the main tool that outputs the known genome size for a given species name or tax ID.
#### Usage
```bash
sizemeup --help
Usage: sizemeup [OPTIONS]
sizemeup - A simple tool to determine the genome size of an organism
╭─ Required Options ────────────────────────────────────────────────────────────────────╮
│ * --query -q TEXT The species name or taxid to determine the size of [required] │
│ * --sizes -z TEXT The built in sizes file to use [required] │
╰───────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ──────────────────────────────────────────────────────────────────╮
│ --outdir -o PATH Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output files [default: sizemeup] │
│ --silent Only critical errors will be printed │
│ --verbose Increase the verbosity of output │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────╯
```
#### Example
```bash
sizemeup --query "Staphylococcus aureus" --silent
Query Result
┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━┓
┃ Name ┃ TaxID ┃ Category ┃ Size ┃ Source ┃ Method ┃
┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━┩
│ Staphylococcus aureus │ 1280 │ bacteria │ 2800000 │ ncbi │ manually-set │
└───────────────────────┴───────┴──────────┴─────────┴────────┴──────────────┘
Writing the genome size to .//sizemeup-sizemeup.txt
sizemeup --query 1280 --silent
Query Result
┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━┓
┃ Name ┃ TaxID ┃ Category ┃ Size ┃ Source ┃ Method ┃
┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━┩
│ Staphylococcus aureus │ 1280 │ bacteria │ 2800000 │ ncbi │ manually-set │
└───────────────────────┴───────┴──────────┴─────────┴────────┴──────────────┘
Writing the genome size to .//sizemeup-sizemeup.txt
```
If the `--query` value is found a table is printed to STDOUT as well as to a file named
`{PREFIX}-sizemeup.txt` where `{PREFIX}` is the value of the `--prefix` option (_default sizemeup_).
Here is an example of the output file:
```tsv
name tax_id category size source method
Staphylococcus aureus 1280 bacteria 2800000 ncbi manually-set
```
However is a species is not found, the you get the following output:
```bash
sizemeup --query "escherichia colis" --silent
2024-09-29 20:24:17 ERROR 2024-09-29 20:24:17:root:ERROR - Could not find 'escherichia colis' in the sizes file, sizemeup.py:138
please consider creating an issue at https://github.com/rpetit3/sizemeup/issues to report
this
Query Result
┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┓
┃ Name ┃ TaxID ┃ Category ┃ Size ┃ Source ┃ Method ┃
┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━┩
│ UNKNOWN_SPECIES │ UNKNOWN_TAXID │ UNKNOWN_CATEGORY │ 0 │ UNKNOWN_SOURCE │ UNKNOWN_METHOD │
└─────────────────┴───────────────┴──────────────────┴──────┴────────────────┴────────────────┘
Writing the genome size to .//sizemeup-sizemeup.txt
```
### `sizemeup-build`
`sizemup-build` is a helper tool used to build the genome size database for `sizemeup`. Do do
this it:
1. Downloads the latest NCBI Assembly Reports
2. Determines species names based on tax id using NCBI Datasets API
3. Merges any user provided genome sizes not available from NCBI
**Note**: This tool isn't necessary for most users, just a simple way to update the database
on your own or at new releases of `sizemeup`.
In the end, it produces a TSV file with the following columns:
- `name` - the species name
- `tax_id` - the NCBI tax id
- `category` - the category of the species (e.g. `bacteria`, `virus`)
- `size` - the genome size in base pairs
- `source` - the source of the genome size (e.g. `ncbi`, `user`)
- `method` - the method used to determine the genome size (e.g. `automatic`, `manual`)
## Citing `sizemeup`
If you make use of `sizemeup` in your analysis, please cite the following:
- __sizemeup__
_Petit III RA, Fearing T, Rowley, C [sizemeup: A simple tool to determine the genome size of an organism](https://github.com/rpetit3/sizemeup) (GitHub)_
## Motivation and Naming
Talking with Taylor, we have a workflow in [Bactopia](https://bactopia.github.io/latest/) called
`teton` for human read scrubbing and taxonomic classification. After running `teton`, the idea
was to run Bactopia to analyze the samples. However, Bactopia requires a genome size for each
sample in order to calculate coverage and a few other metrics. Sure, we could manually look up
the genome size for each sample, that would be tedious and time consuming. We decided to develop
`sizemeup` to handle the looking up genome sizes for us. In addition this paves the way for
users of Bactopia to use `teton` + `sizemeup` to easily mix species within their runs. In other
words, `sizemeup` was built to support the Bactopia workflow (_but you can use it for whatever!_).
As for the name, I wanted something fun and catchy. It's a simple tool to retrieve the genome
size of a given species name, so, I thought "sizemeup" would work!
## Funding
Support for this project came (in part) from the [Wyoming Public Health Division](https://health.wyo.gov/publichealth/).
Raw data
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"description": "[](https://gitpod.io/#https://github.com/rpetit3/sizemeup)\n\n# `sizemeup`\n\n`sizemeup` is a simple tool to retrieve the genome size for a given species name or tax ID. It utilizes\nknown genome sizes available from [NCBI's Assembly Reports](https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_species_genome_size.txt)\nin combination with user provided genome sizes that may not be available from NCBI.\n\n## Contributing\n\nIf you have a species of interest that is not available in the NCBI Assembly Reports, please\nconsider submitting an issue so that we can get it added to `sizemeup`. Otherwise, if you have\nideas to improve `sizemeup` please feel free to!\n\n## Installation\n\nYou can install `sizemeup` using `conda`:\n\n```bash\nconda create -n sizemeup -c conda-forge -c bioconda sizemeup\nconda activate sizemeup\nsizemeup --help\n```\n\n## Available Commands\n\n### `sizemeup`\n\n`sizemeup` is the main tool that outputs the known genome size for a given species name or tax ID.\n\n#### Usage\n\n```bash\nsizemeup --help\n\n Usage: sizemeup [OPTIONS]\n\n sizemeup - A simple tool to determine the genome size of an organism\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --query -q TEXT The species name or taxid to determine the size of [required] \u2502\n\u2502 * --sizes -z TEXT The built in sizes file to use [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --outdir -o PATH Directory to write output [default: ./] \u2502\n\u2502 --prefix -p TEXT Prefix to use for output files [default: sizemeup] \u2502\n\u2502 --silent Only critical errors will be printed \u2502\n\u2502 --verbose Increase the verbosity of output \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n#### Example\n\n```bash\nsizemeup --query \"Staphylococcus aureus\" --silent\n Query Result \n\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2513\n\u2503 Name \u2503 TaxID \u2503 Category \u2503 Size \u2503 Source \u2503 Method \u2503\n\u2521\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2529\n\u2502 Staphylococcus aureus \u2502 1280 \u2502 bacteria \u2502 2800000 \u2502 ncbi \u2502 manually-set \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nWriting the genome size to .//sizemeup-sizemeup.txt\n\nsizemeup --query 1280 --silent\n Query Result \n\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2513\n\u2503 Name \u2503 TaxID \u2503 Category \u2503 Size \u2503 Source \u2503 Method \u2503\n\u2521\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2529\n\u2502 Staphylococcus aureus \u2502 1280 \u2502 bacteria \u2502 2800000 \u2502 ncbi \u2502 manually-set \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nWriting the genome size to .//sizemeup-sizemeup.txt\n```\n\nIf the `--query` value is found a table is printed to STDOUT as well as to a file named\n`{PREFIX}-sizemeup.txt` where `{PREFIX}` is the value of the `--prefix` option (_default sizemeup_).\n\nHere is an example of the output file:\n\n```tsv\nname\ttax_id\tcategory\tsize\tsource\tmethod\nStaphylococcus aureus\t1280\tbacteria\t2800000\tncbi\tmanually-set\n```\n\nHowever is a species is not found, the you get the following output:\n\n```bash\nsizemeup --query \"escherichia colis\" --silent\n2024-09-29 20:24:17 ERROR 2024-09-29 20:24:17:root:ERROR - Could not find 'escherichia colis' in the sizes file, sizemeup.py:138\n please consider creating an issue at https://github.com/rpetit3/sizemeup/issues to report\n this\n Query Result\n\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2513\n\u2503 Name \u2503 TaxID \u2503 Category \u2503 Size \u2503 Source \u2503 Method \u2503\n\u2521\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2529\n\u2502 UNKNOWN_SPECIES \u2502 UNKNOWN_TAXID \u2502 UNKNOWN_CATEGORY \u2502 0 \u2502 UNKNOWN_SOURCE \u2502 UNKNOWN_METHOD \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nWriting the genome size to .//sizemeup-sizemeup.txt\n```\n\n### `sizemeup-build`\n\n`sizemup-build` is a helper tool used to build the genome size database for `sizemeup`. Do do\nthis it:\n\n1. Downloads the latest NCBI Assembly Reports\n2. Determines species names based on tax id using NCBI Datasets API\n3. Merges any user provided genome sizes not available from NCBI\n\n**Note**: This tool isn't necessary for most users, just a simple way to update the database\non your own or at new releases of `sizemeup`.\n\nIn the end, it produces a TSV file with the following columns:\n\n- `name` - the species name\n- `tax_id` - the NCBI tax id\n- `category` - the category of the species (e.g. `bacteria`, `virus`)\n- `size` - the genome size in base pairs\n- `source` - the source of the genome size (e.g. `ncbi`, `user`)\n- `method` - the method used to determine the genome size (e.g. `automatic`, `manual`)\n\n## Citing `sizemeup`\nIf you make use of `sizemeup` in your analysis, please cite the following:\n\n- __sizemeup__ \n_Petit III RA, Fearing T, Rowley, C [sizemeup: A simple tool to determine the genome size of an organism](https://github.com/rpetit3/sizemeup) (GitHub)_ \n\n## Motivation and Naming\n\nTalking with Taylor, we have a workflow in [Bactopia](https://bactopia.github.io/latest/) called\n`teton` for human read scrubbing and taxonomic classification. After running `teton`, the idea\nwas to run Bactopia to analyze the samples. However, Bactopia requires a genome size for each\nsample in order to calculate coverage and a few other metrics. Sure, we could manually look up\nthe genome size for each sample, that would be tedious and time consuming. We decided to develop\n`sizemeup` to handle the looking up genome sizes for us. In addition this paves the way for\nusers of Bactopia to use `teton` + `sizemeup` to easily mix species within their runs. In other\nwords, `sizemeup` was built to support the Bactopia workflow (_but you can use it for whatever!_).\n\nAs for the name, I wanted something fun and catchy. It's a simple tool to retrieve the genome\nsize of a given species name, so, I thought \"sizemeup\" would work!\n\n## Funding\n\nSupport for this project came (in part) from the [Wyoming Public Health Division](https://health.wyo.gov/publichealth/).\n\n\n\n",
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