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: deci [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:
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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Publisher:
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refs/tags/cli-v1.0.4 - Owner: https://github.com/EBI-Metagenomics
- Access:
public
- Token Issuer:
https://token.actions.githubusercontent.com - Runner Environment:
github-hosted - Publication workflow:
release-cli.yml@03d6479f9ee1326637fb23b2f288212f7798cf37 - Trigger Event:
push
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