Individually annotate long, error-prone nucleotide sequences into proteins
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.
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.
pipx install deciphon
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. │
╰──────────────────────────────────────────────────────────────────────────────╯
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
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FAQs
Individually annotate long, error-prone nucleotide sequences into proteins
We found that deciphon demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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