Metadata-Version: 2.1
Name: deciphon
Version: 0.12.1
Summary: Individually annotate long, error-prone nucleotide sequences into proteins
License: MIT
Author: Danilo Horta
Author-email: horta@ebi.ac.uk
Requires-Python: >=3.9,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: cffi (>=1.15.1,<2.0.0)
Requires-Dist: deciphon-core (>=0.22.1)
Requires-Dist: deciphon-snap (>=0.9.1)
Requires-Dist: fasta-reader (>=3,<4)
Requires-Dist: h3daemon (>=0.13.8)
Requires-Dist: hmmer (>=0,<1)
Requires-Dist: ijson (>=3.2.3,<4.0.0)
Requires-Dist: pydantic (>=2,<3)
Requires-Dist: rich (>=13,<14)
Requires-Dist: typer (>=0,<1)
Description-Content-Type: text/markdown

# 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!

