Individually annotate long, error-prone nucleotide sequences into proteins
Project description
Welcome to deciphon ๐
Individually annotate long, error-prone nucleotide sequences into proteins
๐ Homepage
โก๏ธ 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
๐ก 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
๐ก You might need to close your terminal and reopen it for the changes to take effect.
Install
pipx install deciphon
Usage
Usage: dcp [OPTIONS] COMMAND [ARGS]...
โญโ Options โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฎ
โ --version โ
โ --help Show this message and exit. โ
โฐโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
โญโ Commands โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฎ
โ press Press HMM ASCII file into a Deciphon database one. โ
โ scan Annotate nucleotide sequences into proteins a protein database. โ
โฐโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
Example
Download the minifam.hmm protein database:
pipx run blx get \
fe305d9c09e123f987f49b9056e34c374e085d8831f815cc73d8ea4cdec84960 \
minifam.hmm
Download the consensus.json file of sequences:
pipx run blx get \
af483ed5aa42010e8f6c950c42d81bac69f995876bf78a5965f319e83dc3923e \
consensus.hmm
Press it:
dcp press minifam.hmm
Scan it:
dcp scan minifam.hmm consensus.json
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