deciphon 0.14.0

Individually annotate long, error-prone nucleotide sequences into proteins

Welcome to deciphon 👋

Individually annotate long, error-prone nucleotide sequences into proteins

🏠 Homepage

⚡️ Requirements

• Python >= 3.9
• Pip
• Podman >= 3.4
• Homebrew on MacOS (recommended)
• Pipx for Python package management (recommended)

MacOS

Install Python and Podman:

brew update && brew install python podman 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 and Podman:

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:

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: 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:

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):

deci press minifam.hmm 1

Scan it:

deci scan minifam.hmm sequences.fna

Show it:

deci see sequences.dcs

👤 Author

• Danilo Horta

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