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 >= 3.11
- 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
๐ก 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
๐ก 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]...
โญโ Options โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฎ
โ --version Show version. โ
โ --help Show this message and exit. โ
โฐโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
โญโ Commands โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฎ
โ press Make protein database. โ
โ scan Scan nucleotide sequence against protein database. โ
โ see Display scan results. โ
โ worker Launch worker. โ
โฐโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
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
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refs/tags/cli-v1.0.13 - Owner: https://github.com/EBI-Metagenomics
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