| Name | genome-uploader JSON |
| Version |
2.5.0
JSON |
| download |
| home_page | None |
| Summary | Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This script generates xmls and manifests necessary for submission with webin-cli. |
| upload_time | 2025-10-08 04:13:06 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | Apache Software License 2.0 |
| keywords |
bioinformatics
tool
metagenomics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Public bins and MAGs uploader
This repository allows to:
* Generate xmls and manifests necessary for genome submission
* Link the genomes you want to submit with the samples/runs used to generate them
* Upload bins and MAGs in fasta format to ENA (European Nucleotide Archive) with webin-cli
## How it works
When you submit genomes to the [ENA](https://www.ebi.ac.uk/ena/browser/home), you need to register a sample for every genome containing all the relevant metadata describing the genome and the sample of origin. The `genome_uploader` acts as the main linker to preserve sample metadata as much as possible. For every genome to register, you need an INSDC run or assembly accession associated to the genome in order for the script to inherit its relevant metadata. On top of those metadata, the script adds metadata specified by the user that are specific to the genome, like taxonomy, statistics, or the tools used to generate it. The metadata that ENA requires are descibed in the checklist for [MAGs](<https://www.ebi.ac.uk/ena/browser/view/ERC000050>) and for [bins](<https://www.ebi.ac.uk/ena/browser/view/ERC000047>), respectively.
### Input tsv and fields
The genome_uploader takes as input one tsv (tab-separated values) table in the following format:
| genome_name | genome_path | accessions | assembly_software | binning_software | binning_parameters | stats_generation_software | completeness | contamination | genome_coverage | metagenome | co-assembly | broad_environment | local_environment | environmental_medium | rRNA_presence | taxonomy_lineage |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| ERR4647712_crispatus | path/to/ERR4647712.fa.gz | ERR4647712 | megahit_v1.2.9 | MGnify-genomes-generation-pipeline_v1.0.0 | default | CheckM2_v1.0.1 | 100 | 0.38 | 14.2 | chicken gut metagenome | False | chicken | gut | mucosa | True | d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus crispatus |
With columns indicating:
* _genome_name_: genome id (unique string identifier)
* _accessions_: run(s) or assembly(ies) the genome was generated from (DRR/ERR/SRRxxxxxx for runs, DRZ/ERZ/SRZxxxxxx for assemblies). If the genome was generated by a co-assembly of multiple runs, separate them with a comma.
* _assembly_software_: assemblerName_vX.X
* _binning_software_: binnerName_vX.X
* _binning_parameters_: binning parameters
* _stats_generation_software_: software_vX.X
* _completeness_: `float`
* _contamination_: `float`
* _rRNA_presence_: `True/False` if all among 5S, 16S, and 23S genes, and at least 18 tRNA genes, have been detected in the genome
* _NCBI_lineage_: full NCBI lineage - format: `x;y;z;...`. The same organism can be described in two different ways: either in tax ids (`integers`) or `strings`. For example, the lineage for _E. coli_ can be:
* `Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia`
* `2;1224;1236;91347;543;561;562`
* _metagenome_: needs to be listed in the taxonomy tree [here](<https://www.ebi.ac.uk/ena/browser/view/408169?show=tax-tree>) (you might need to press "Tax tree - Show" in the right most section of the page)
* _co-assembly_: `True/False`, whether the genome was generated from a co-assembly. N.B. the script only supports co-assemblies generated from the same project.
* _genome_coverage_ : genome coverage against raw reads
* _genome_path_: path to genome to upload (already compressed)
* _broad_environment_: `string` (explanation following)
* _local_environment_: `string` (explanation following)
* _environmental_medium_: `string` (explanation following)
According to ENA checklist's guidelines, `broad_environment` describes the broad ecological context of a sample - desert, taiga, coral reef, ... `local_environment` is more local - lake, harbour, cliff, ... `environmental_medium` is either the material displaced by the sample, or the one in which the sample was embedded prior to the sampling event - air, soil, water, ...
For host-associated metagenomic samples, the three variables can be defined similarly to the following example for the chicken gut metagenome: "chicken digestive system", "digestive tube", "caecum". More information can be found at [ERC000050](<https://www.ebi.ac.uk/ena/browser/view/ERC000050>) for bins and [ERC000047](<https://www.ebi.ac.uk/ena/browser/view/ERC000047>) for MAGs under field names "broad-scale environmental context", "local environmental context", "environmental medium"
An example of input tsv table can be found [here](examples/input_example.tsv)
## _Warnings_
### Mandatory vs Optional Fields
All fields above are mandatory for MAG submission (see ENA's MAGs checklist [here](<https://www.ebi.ac.uk/ena/browser/view/ERC000047>)). However, if you are registering bins, you cand decide whether to omit the following fields: `completeness`, `contamination` and `rRNA_presence`(see ENA's bins checklist [here](<https://www.ebi.ac.uk/ena/browser/view/ERC000050>)). These values are used together to determine MAG quality according to MIMAG criteria (described [here](https://www.nature.com/articles/nbt.3893/tables/1)).
If you already generated these for your bins, our recommendation is to include them for shareability and to describe your sample more accurately.
### Existing accessions in the INSDC
Raw-read runs or assemblies from which genomes were generated should already be available on the INSDC (ENA by EBI, GenBank by NCBI, or DDBJ) for this script to work. Therefore, at least a DRR|ERR|SRR accession (for runs) or a ERZ|SRZ|DRZ accession (for assemblies) should be available.
If you are working with your own, private data on ENA, you will need to add the `--private` flag to access private metadata through ENA API. This implies that if you are working on public data, you can omit the flag. However, you will need to submit two different batches of data if you are handling both private and public data.
### TPA generation and upload
If uploading TPA (Third PArty) genomes, you will need to contact [ENA support](<https://www.ebi.ac.uk/ena/browser/support>) before using the script. They will provide instructions on how to correctly register a TPA project where to submit your genomes. If both TPA and non-TPA genomes need to be uploaded, please divide them in two batches and use the `--tpa` flag only with TPA genomes.
### Compress your fasta files
Files to be uploaded will need to be compressed (e.g. already in .gz format).
### Split your input tables
No more than 5000 genomes can be submitted at the same time. If you have more than 5000, split your table into smaller ones and launch the `genome_uploader` for each table.
## Installation and setup
You can install **genome_uploader** with:
```bash
pip install genome_uploader
```
Next download webin-cli for upload to **ENA** with:
```bash
download_webin_cli -v 8.2.0
# we recommend using the most recent version of webin-cli
```
## Setting ENA Credentials
This tool requires your ENA Webin credentials to function. You can provide these by setting environment variables or using an environment file.
### Using an environment file
Create a file named `.env` in your home directory (`~/.env`), your current working directory (`./.env`), or specify a custom file (default is `.env`).
Add the following lines with your credentials:
```env
ENA_WEBIN=your_username_here
ENA_WEBIN_PASSWORD=your_password_here
```
### Alternatively, set the environment variables directly in your shell
```bash
export ENA_WEBIN=your_username_here
export ENA_WEBIN_PASSWORD=your_password_here
```
## Command examples
You can generate pre-upload files with:
```bash
genome_upload -u UPLOAD_STUDY --genome_info METADATA_FILE (--mags | --bins) --centre_name CENTRE_NAME [--out] [--force] [--live] [--tpa]
```
where
* `-u UPLOAD_STUDY`: study accession for genomes upload to ENA (in format ERPxxxxxx or PRJEBxxxxxx)
* `---genome_info METADATA_FILE` : genomes metadata file in tsv format
* `-m, --mags, --b, --bins`: select for bin or MAG upload. If in doubt, check [which definition fits best according to ENA](<https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome.html>)
* `--out`: output folder (default: working directory)
* `--force`: forces reset of sample xmls generation. This is useful if you changed something in your tsv table, or if ENA metadata haven't been downloaded correctly (you can check this in `ENA_backup.json`).
* `--live`: registers genomes on ENA's live server. Omitting this option allows to validate samples beforehand (it will need the `-test` option in the upload command for the test submission to work)
* `--centre_name CENTRE_NAME`: name of the centre generating and uploading genomes
* `--tpa`: if uploading TPA (Third PArty) generated genomes
* `--private`: if data is private
It is recommended to validate your genomes in test mode (i.e. without `--live` in the registration step and with `-test` during the upload) before attempting the final upload. Launching the registration in test mode will add a timestamp to the genome name to allow multiple executions of the test process.
Sample xmls won't be regenerated automatically if a previous xml already exists. If any metadata or value in the tsv table changes, `--force` will allow xml regeneration.
### Produced files:
The script produces the following files and folders:
```bash
bin_upload/MAG_upload
├── manifests
│ └── ...
├── manifests_test # folder generated for validation in test mode
│ └── ...
├── ENA_backup.json # backup file to prevent re-download of metadata from ENA. Regeneration can be forced with --force
├── genome_samples.xml # xml generated to register samples on ENA before the upload
├── registered_bins/MAGs.tsv # list of genomes registered on ENA in live mode - needed for manifest generation
├── registered_bins/MAGs_test.tsv # list of genomes registered on ENA in test mode - needed for manifest generation
└── submission.xml # xml used for genome registration on ENA
```
An example of output files and folder structure submitted in test mode can be found under the `examples` folder.
## Upload genomes
Once manifest files are generated, it is necessary to use ENA's webin-cli resource to upload genomes.
To test your submission (i.e. you registered your samples without the `--live` option with genome_upload.py), add the `-test` argument.
A live execution example within this repo is the following:
```bash
java -jar ./webin-cli.jar \
-context=genome \
-manifest=ERR123456_bin.1.manifest \
-userName="Webin-XXX" \
-password="YYY" \
-submit
```
More information on ENA's webin-cli can be found [here](<https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html>).
## Devs section
### Testing submission in normal mode vs strict submission
ENA's test servers reset every day. This means that if you try to register the same set of samples more than once in a single day, the request will fail because the automatically generated aliases would result as duplicates on ENA's servers. To prevent this issue, when you register samples in test mode, the `genome_uploader` appends a timestamp to each generated alias. This ensures that you can repeat your tests multiple times without running into duplicate-alias errors.
However, when debugging or checking the script’s behavior in development mode, you might want the aliases to remain consistent across runs, so that repeated submissions refer to the same sample. To allow this, you can use the `--test-suffix` flag when running `genome_upload.py`, which lets you define a custom suffix instead of the automatic timestamp. This gives you more control over how sample aliases are generated during testing.
Raw data
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"description": "# Public bins and MAGs uploader\nThis repository allows to:\n\n * Generate xmls and manifests necessary for genome submission\n * Link the genomes you want to submit with the samples/runs used to generate them\n * Upload bins and MAGs in fasta format to ENA (European Nucleotide Archive) with webin-cli \n\n## How it works\n\nWhen you submit genomes to the [ENA](https://www.ebi.ac.uk/ena/browser/home), you need to register a sample for every genome containing all the relevant metadata describing the genome and the sample of origin. The `genome_uploader` acts as the main linker to preserve sample metadata as much as possible. For every genome to register, you need an INSDC run or assembly accession associated to the genome in order for the script to inherit its relevant metadata. On top of those metadata, the script adds metadata specified by the user that are specific to the genome, like taxonomy, statistics, or the tools used to generate it. The metadata that ENA requires are descibed in the checklist for [MAGs](<https://www.ebi.ac.uk/ena/browser/view/ERC000050>) and for [bins](<https://www.ebi.ac.uk/ena/browser/view/ERC000047>), respectively.\n\n### Input tsv and fields\nThe genome_uploader takes as input one tsv (tab-separated values) table in the following format:\n\n| genome_name | genome_path | accessions | assembly_software | binning_software | binning_parameters | stats_generation_software | completeness | contamination | genome_coverage | metagenome | co-assembly | broad_environment | local_environment | environmental_medium | rRNA_presence | taxonomy_lineage |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| ERR4647712_crispatus | path/to/ERR4647712.fa.gz | ERR4647712 | megahit_v1.2.9 | MGnify-genomes-generation-pipeline_v1.0.0 | default | CheckM2_v1.0.1 | 100 | 0.38 | 14.2 | chicken gut metagenome | False | chicken | gut | mucosa | True | d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus crispatus |\n\nWith columns indicating:\n * _genome_name_: genome id (unique string identifier)\n * _accessions_: run(s) or assembly(ies) the genome was generated from (DRR/ERR/SRRxxxxxx for runs, DRZ/ERZ/SRZxxxxxx for assemblies). If the genome was generated by a co-assembly of multiple runs, separate them with a comma.\n * _assembly_software_: assemblerName_vX.X\n * _binning_software_: binnerName_vX.X\n * _binning_parameters_: binning parameters\n * _stats_generation_software_: software_vX.X\n * _completeness_: `float`\n * _contamination_: `float`\n * _rRNA_presence_: `True/False` if all among 5S, 16S, and 23S genes, and at least 18 tRNA genes, have been detected in the genome\n * _NCBI_lineage_: full NCBI lineage - format: `x;y;z;...`. The same organism can be described in two different ways: either in tax ids (`integers`) or `strings`. For example, the lineage for _E. coli_ can be:\n * `Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia`\n * `2;1224;1236;91347;543;561;562`\n * _metagenome_: needs to be listed in the taxonomy tree [here](<https://www.ebi.ac.uk/ena/browser/view/408169?show=tax-tree>) (you might need to press \"Tax tree - Show\" in the right most section of the page)\n * _co-assembly_: `True/False`, whether the genome was generated from a co-assembly. N.B. the script only supports co-assemblies generated from the same project.\n * _genome_coverage_ : genome coverage against raw reads\n * _genome_path_: path to genome to upload (already compressed)\n * _broad_environment_: `string` (explanation following)\n * _local_environment_: `string` (explanation following)\n * _environmental_medium_: `string` (explanation following)\n\nAccording to ENA checklist's guidelines, `broad_environment` describes the broad ecological context of a sample - desert, taiga, coral reef, ... `local_environment` is more local - lake, harbour, cliff, ... `environmental_medium` is either the material displaced by the sample, or the one in which the sample was embedded prior to the sampling event - air, soil, water, ...\nFor host-associated metagenomic samples, the three variables can be defined similarly to the following example for the chicken gut metagenome: \"chicken digestive system\", \"digestive tube\", \"caecum\". More information can be found at [ERC000050](<https://www.ebi.ac.uk/ena/browser/view/ERC000050>) for bins and [ERC000047](<https://www.ebi.ac.uk/ena/browser/view/ERC000047>) for MAGs under field names \"broad-scale environmental context\", \"local environmental context\", \"environmental medium\"\n\nAn example of input tsv table can be found [here](examples/input_example.tsv)\n\n## _Warnings_\n\n### Mandatory vs Optional Fields\nAll fields above are mandatory for MAG submission (see ENA's MAGs checklist [here](<https://www.ebi.ac.uk/ena/browser/view/ERC000047>)). However, if you are registering bins, you cand decide whether to omit the following fields: `completeness`, `contamination` and `rRNA_presence`(see ENA's bins checklist [here](<https://www.ebi.ac.uk/ena/browser/view/ERC000050>)). These values are used together to determine MAG quality according to MIMAG criteria (described [here](https://www.nature.com/articles/nbt.3893/tables/1)).\n\nIf you already generated these for your bins, our recommendation is to include them for shareability and to describe your sample more accurately.\n\n### Existing accessions in the INSDC\nRaw-read runs or assemblies from which genomes were generated should already be available on the INSDC (ENA by EBI, GenBank by NCBI, or DDBJ) for this script to work. Therefore, at least a DRR|ERR|SRR accession (for runs) or a ERZ|SRZ|DRZ accession (for assemblies) should be available. \n\nIf you are working with your own, private data on ENA, you will need to add the `--private` flag to access private metadata through ENA API. This implies that if you are working on public data, you can omit the flag. However, you will need to submit two different batches of data if you are handling both private and public data.\n\n### TPA generation and upload\nIf uploading TPA (Third PArty) genomes, you will need to contact [ENA support](<https://www.ebi.ac.uk/ena/browser/support>) before using the script. They will provide instructions on how to correctly register a TPA project where to submit your genomes. If both TPA and non-TPA genomes need to be uploaded, please divide them in two batches and use the `--tpa` flag only with TPA genomes.\n\n### Compress your fasta files\nFiles to be uploaded will need to be compressed (e.g. already in .gz format).\n\n### Split your input tables\nNo more than 5000 genomes can be submitted at the same time. If you have more than 5000, split your table into smaller ones and launch the `genome_uploader` for each table.\n\n## Installation and setup\n\nYou can install **genome_uploader** with:\n\n```bash\npip install genome_uploader\n```\n\nNext download webin-cli for upload to **ENA** with:\n\n```bash\ndownload_webin_cli -v 8.2.0\n# we recommend using the most recent version of webin-cli\n```\n\n## Setting ENA Credentials\n\nThis tool requires your ENA Webin credentials to function. You can provide these by setting environment variables or using an environment file.\n\n### Using an environment file\n\nCreate a file named `.env` in your home directory (`~/.env`), your current working directory (`./.env`), or specify a custom file (default is `.env`).\n\nAdd the following lines with your credentials:\n\n```env\nENA_WEBIN=your_username_here\nENA_WEBIN_PASSWORD=your_password_here\n```\n\n### Alternatively, set the environment variables directly in your shell\n\n```bash\nexport ENA_WEBIN=your_username_here\nexport ENA_WEBIN_PASSWORD=your_password_here\n```\n\n## Command examples\nYou can generate pre-upload files with:\n\n```bash\ngenome_upload -u UPLOAD_STUDY --genome_info METADATA_FILE (--mags | --bins) --centre_name CENTRE_NAME [--out] [--force] [--live] [--tpa]\n```\n\nwhere\n * `-u UPLOAD_STUDY`: study accession for genomes upload to ENA (in format ERPxxxxxx or PRJEBxxxxxx)\n * `---genome_info METADATA_FILE` : genomes metadata file in tsv format\n * `-m, --mags, --b, --bins`: select for bin or MAG upload. If in doubt, check [which definition fits best according to ENA](<https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome.html>)\n * `--out`: output folder (default: working directory)\n * `--force`: forces reset of sample xmls generation. This is useful if you changed something in your tsv table, or if ENA metadata haven't been downloaded correctly (you can check this in `ENA_backup.json`).\n * `--live`: registers genomes on ENA's live server. Omitting this option allows to validate samples beforehand (it will need the `-test` option in the upload command for the test submission to work)\n * `--centre_name CENTRE_NAME`: name of the centre generating and uploading genomes\n * `--tpa`: if uploading TPA (Third PArty) generated genomes\n * `--private`: if data is private\n\nIt is recommended to validate your genomes in test mode (i.e. without `--live` in the registration step and with `-test` during the upload) before attempting the final upload. Launching the registration in test mode will add a timestamp to the genome name to allow multiple executions of the test process.\n\nSample xmls won't be regenerated automatically if a previous xml already exists. If any metadata or value in the tsv table changes, `--force` will allow xml regeneration.\n\n### Produced files:\nThe script produces the following files and folders:\n```bash\nbin_upload/MAG_upload\n\u251c\u2500\u2500 manifests\n\u2502 \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 manifests_test # folder generated for validation in test mode\n\u2502 \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 ENA_backup.json # backup file to prevent re-download of metadata from ENA. Regeneration can be forced with --force\n\u251c\u2500\u2500 genome_samples.xml # xml generated to register samples on ENA before the upload\n\u251c\u2500\u2500 registered_bins/MAGs.tsv # list of genomes registered on ENA in live mode - needed for manifest generation\n\u251c\u2500\u2500 registered_bins/MAGs_test.tsv # list of genomes registered on ENA in test mode - needed for manifest generation\n\u2514\u2500\u2500 submission.xml # xml used for genome registration on ENA\n```\n\nAn example of output files and folder structure submitted in test mode can be found under the `examples` folder.\n\n## Upload genomes\nOnce manifest files are generated, it is necessary to use ENA's webin-cli resource to upload genomes.\n\nTo test your submission (i.e. you registered your samples without the `--live` option with genome_upload.py), add the `-test` argument.\n\nA live execution example within this repo is the following:\n```bash\njava -jar ./webin-cli.jar \\\n -context=genome \\\n -manifest=ERR123456_bin.1.manifest \\\n -userName=\"Webin-XXX\" \\\n -password=\"YYY\" \\\n -submit\n```\n\nMore information on ENA's webin-cli can be found [here](<https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html>).\n\n## Devs section\n\n### Testing submission in normal mode vs strict submission\nENA's test servers reset every day. This means that if you try to register the same set of samples more than once in a single day, the request will fail because the automatically generated aliases would result as duplicates on ENA's servers. To prevent this issue, when you register samples in test mode, the `genome_uploader` appends a timestamp to each generated alias. This ensures that you can repeat your tests multiple times without running into duplicate-alias errors.\n\nHowever, when debugging or checking the script\u2019s behavior in development mode, you might want the aliases to remain consistent across runs, so that repeated submissions refer to the same sample. To allow this, you can use the `--test-suffix` flag when running `genome_upload.py`, which lets you define a custom suffix instead of the automatic timestamp. This gives you more control over how sample aliases are generated during testing.\n",
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