Welcome to deciphon 👋

Individually annotate long, error-prone nucleotide sequences into proteins

🏠 Homepage

⚡️ Requirements

Python >= 3.11
Pip
Homebrew on MacOS (recommended)
Pipx (or uvx) for Python application management (recommended)

MacOS

Install Python and Pipx:

brew update && brew install python pipx

Ensure that your PATH environment variable is all set:

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:

sudo apt update && \
    sudo apt install python3 python3-pip python3-venv --yes && \
    python3 -m pip install --user pipx

Ensure that your PATH environment variable is all set:

python3 -m pipx ensurepath

💡 You might need to close your terminal and reopen it for the changes to take effect.

Install

pipx install deciphon

Usage

 Usage: deciphon [OPTIONS] COMMAND [ARGS]...

╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --version          Show version.                                             │
│ --help             Show this message and exit.                               │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────╮
│ press    Make protein database.                                              │
│ scan     Scan nucleotide sequence against protein database.                  │
│ see      Display scan results.                                               │
│ worker   Launch worker.                                                      │
╰──────────────────────────────────────────────────────────────────────────────╯

Example

Download the minifam.hmm protein database:

curl -O https://raw.githubusercontent.com/EBI-Metagenomics/deciphon/main/cli/tests/files/minifam.hmm

Download the consensus.fna file of sequences:

curl -O https://raw.githubusercontent.com/EBI-Metagenomics/deciphon/main/cli/tests/files/sequences.fna

Press it (using The Standard Code):

deciphon press minifam.hmm 1

Scan it:

deciphon scan minifam.hmm sequences.fna

Show it:

deciphon see sequences.dcs

👤 Author

Danilo Horta

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Metadata

Release files for deciphon 1.0.13

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for deciphon 1.0.13
File	Size	Uploaded
deciphon-1.0.13.tar.gz	11.5 kB	Mar 9, 2025	Details

Built distribution (wheel)

Table of built distributions (wheels) for deciphon 1.0.13
File	Interpreter	ABI	Platform	Reset
deciphon-1.0.13-py3-none-any.whl 12.9 kB Mar 9, 2025	Python 3	none	any	Details

Total release size: 24.4 kB

Release files / deciphon-1.0.13.tar.gz

Download URL	deciphon-1.0.13.tar.gz
Size	11.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`5d520a28ab975f0db01d72430aa9ef8fb9732b60215059ed6a48c174bce60dee`
BLAKE2b-256 checksum How to use checksums	`70a0d53945f2377661a754a7ddeda7ae2ae1ef207ce8ac50e0fd5018841f547f`
Upload date	Mar 9, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/EBI-Metagenomics/deciphon
Publishing commit: github.com/EBI-Metagenomics/deciphon/tree/75a529c53c16659c020d1c8b602bab2de98dd289

Workflow

Publishing configuration: github.com/EBI-Metagenomics/deciphon/blob/75a529c53c16659c020d1c8b602bab2de98dd289/.github/workflows/release-cli.yml
Publishing logs: github.com/EBI-Metagenomics/deciphon/actions/runs/13747863614/attempts/1

Artifact

Subject: deciphon-1.0.13.tar.gz
SHA-256 checksum: 5d520a28ab975f0db01d72430aa9ef8fb9732b60215059ed6a48c174bce60dee Verifying attestations

Release files / deciphon-1.0.13-py3-none-any.whl

Download URL	deciphon-1.0.13-py3-none-any.whl
Size	12.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`4476f9c025f8465f0267302bc67ed155a2aaa3b1513c4e313cdf1bea1c420ea5`
BLAKE2b-256 checksum How to use checksums	`c7c38863b1aef67d9e6b53f392e46f947fad3de50c14fd38e67ffd70110aeae8`
Upload date	Mar 9, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/EBI-Metagenomics/deciphon
Publishing commit: github.com/EBI-Metagenomics/deciphon/tree/75a529c53c16659c020d1c8b602bab2de98dd289

Workflow

Publishing configuration: github.com/EBI-Metagenomics/deciphon/blob/75a529c53c16659c020d1c8b602bab2de98dd289/.github/workflows/release-cli.yml
Publishing logs: github.com/EBI-Metagenomics/deciphon/actions/runs/13747863614/attempts/1

Artifact

Subject: deciphon-1.0.13-py3-none-any.whl
SHA-256 checksum: 4476f9c025f8465f0267302bc67ed155a2aaa3b1513c4e313cdf1bea1c420ea5 Verifying attestations