| Name | deciphon JSON |
| Version |
0.14.0
JSON |
| download |
| home_page | None |
| Summary | Individually annotate long, error-prone nucleotide sequences into proteins |
| upload_time | 2024-09-26 15:46:50 |
| maintainer | None |
| docs_url | None |
| author | Danilo Horta |
| requires_python | <4.0,>=3.9 |
| license | MIT |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Welcome to deciphon 👋
> Individually annotate long, error-prone nucleotide sequences into proteins
### 🏠 [Homepage](https://github.com/EBI-Metagenomics/deciphon-py)
## ⚡️ Requirements
- Python >= 3.9
- Pip
- [Podman](https://podman.io) >= 3.4
- [Homebrew](https://brew.sh) on MacOS (recommended)
- [Pipx](https://pypa.github.io/pipx/) for Python package management (recommended)
### MacOS
Install Python and Podman:
```sh
brew update && brew install python podman pipx
```
Ensure that your `PATH` environment variable is all set:
```sh
pipx ensurepath
```
💡 You might need to close your terminal and reopen it for the changes to take effect.
### Ubuntu (and Debian-based distros)
Install Python and Podman:
```sh
sudo apt update && \
sudo apt install python3 python3-pip python3-venv podman --yes && \
python3 -m pip install --user pipx
```
Ensure that your `PATH` environment variable is all set:
```sh
python3 -m pipx ensurepath
```
💡 You might need to close your terminal and reopen it for the changes to take effect.
## Install
```sh
pipx install deciphon
```
## Usage
```
Usage: deci [OPTIONS] COMMAND [ARGS]...
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --version │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────╮
│ press Press HMM ASCII file into a Deciphon database one. │
│ scan Annotate nucleotide sequences into proteins a protein database. │
╰──────────────────────────────────────────────────────────────────────────────╯
```
## Example
Download the `minifam.hmm` protein database:
```sh
curl -O https://raw.githubusercontent.com/EBI-Metagenomics/deciphon/main/cli/tests/files/minifam.hmm
```
Download the `consensus.fna` file of sequences:
```sh
curl -O https://raw.githubusercontent.com/EBI-Metagenomics/deciphon/main/cli/tests/files/sequences.fna
```
Press it (using The Standard Code):
```sh
deci press minifam.hmm 1
```
Scan it:
```sh
deci scan minifam.hmm sequences.fna
```
Show it:
```sh
deci see sequences.dcs
```
## 👤 Author
- [Danilo Horta](https://github.com/horta)
## Show your support
Give a ⭐️ if this project helped you!
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"description": "# Welcome to deciphon \ud83d\udc4b\n\n> Individually annotate long, error-prone nucleotide sequences into proteins\n\n### \ud83c\udfe0 [Homepage](https://github.com/EBI-Metagenomics/deciphon-py)\n\n## \u26a1\ufe0f Requirements\n\n- Python >= 3.9\n- Pip\n- [Podman](https://podman.io) >= 3.4\n- [Homebrew](https://brew.sh) on MacOS (recommended)\n- [Pipx](https://pypa.github.io/pipx/) for Python package management (recommended)\n\n### MacOS\n\nInstall Python and Podman:\n\n```sh\nbrew update && brew install python podman pipx\n```\n\nEnsure that your `PATH` environment variable is all set:\n\n```sh\npipx ensurepath\n```\n\n\ud83d\udca1 You might need to close your terminal and reopen it for the changes to take effect.\n\n### Ubuntu (and Debian-based distros)\n\nInstall Python and Podman:\n\n```sh\nsudo apt update && \\\n sudo apt install python3 python3-pip python3-venv podman --yes && \\\n python3 -m pip install --user pipx\n```\n\nEnsure that your `PATH` environment variable is all set:\n\n```sh\npython3 -m pipx ensurepath\n```\n\n\ud83d\udca1 You might need to close your terminal and reopen it for the changes to take effect.\n\n## Install\n\n```sh\npipx install deciphon\n```\n\n## Usage\n\n```\n Usage: deci [OPTIONS] COMMAND [ARGS]...\n\n\u256d\u2500 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 --version \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\u256f\n\u256d\u2500 Commands \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 press Press HMM ASCII file into a Deciphon database one. \u2502\n\u2502 scan Annotate nucleotide sequences into proteins a protein database. \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\u256f\n```\n\n## Example\n\nDownload the `minifam.hmm` protein database:\n\n```sh\ncurl -O https://raw.githubusercontent.com/EBI-Metagenomics/deciphon/main/cli/tests/files/minifam.hmm\n```\n\nDownload the `consensus.fna` file of sequences:\n\n```sh\ncurl -O https://raw.githubusercontent.com/EBI-Metagenomics/deciphon/main/cli/tests/files/sequences.fna\n```\n\nPress it (using The Standard Code):\n\n```sh\ndeci press minifam.hmm 1\n```\n\nScan it:\n\n```sh\ndeci scan minifam.hmm sequences.fna\n```\n\nShow it:\n\n```sh\ndeci see sequences.dcs\n```\n\n## \ud83d\udc64 Author\n\n- [Danilo Horta](https://github.com/horta)\n\n## Show your support\n\nGive a \u2b50\ufe0f if this project helped you!\n\n",
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