# genome_update
genome_update is a package that downloads genomes from NCBI and saves information about them in a yaml file. It can also use a local yaml file to update and download new genomes.
Sequence statistics is also calculated for each genome and added to the yaml file.
## Getting Started
These instructions will provide information how to install and use the software.
### Prerequisites
Python Pandas PyYaml
### How to install
To install Genome_update you can either download source code directly from github and build it your self, an easier alternative is to use pip.
Installing by pip:
` pip install genome_update ` Pip will also install all prerequisities. It is also recommended to update all prerequisities.
Installing genome_update and upgrading prerequisities:
` pip install genome_update --upgrade `
### Usage
Download all genomes from a specific genus: ` genome_update -g <Genus> `
Download all genomes from a specific genus, but much faster: ` genome_update -g <Genus> -p <threads> `
Download all genomes from a specific genus, but much faster, to a specific directory (default is /genomes): ` genome_update -g <Genus> -p <threads> -o <directory> `
Download all genomes from a specific species: ` genome_update -g <Genus> -s <species_taxid> `
To update a local yaml file: ` genome_update -u -i <yamlfile> `
To download missing genomes from a local yaml file: ` genome_update -d -i <yamlfile> `
To download genomes from another domain than bacteria: ` genome_update -domain <domain> -g <Genus> `
## Authors
Emil Samuelsson - Initial work - [Emisam](https://github.com/Emisam)
## License
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
## Acknowledgments
Would like to thank kblin for his amazing work with the ncbi_genome_download which provided lots of inspiration when writing genome_update.
1 maintainer
Release files for genome-update 0.1.6.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| genome_update-0.1.6.8.tar.gz | 6.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| genome_update-0.1.6.8-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 16.8 kB
Release files / genome_update-0.1.6.8.tar.gz
| Download URL | genome_update-0.1.6.8.tar.gz |
|---|---|
| Size | 6.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
816a68f695388cbd452863016dc1e0dcc5b6699f6c301293a6894de00188ad1f
|
|
BLAKE2b-256 checksum How to use checksums |
fb3186bc6828581516b15954c6122e95d014f7c3de4b129bf450661a68c5e010
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Release files / genome_update-0.1.6.8-py2.py3-none-any.whl
| Download URL | genome_update-0.1.6.8-py2.py3-none-any.whl |
|---|---|
| Size | 10.4 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
6fefe134a989dc03b09b92ef512b150f63d2493c4617e78e6510c31c868e846e
|
|
BLAKE2b-256 checksum How to use checksums |
123ebf24e6ad4dee912a09f289099f8388fd502d6e467141b5f4d5d973fefa84
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
