A Python package for RNA Motif Library creation.
preprint: (insert paper link here)
A default CSV (nrlist_3.262_3.5A.csv) is in the directory data/csvs.
Make sure to download the most recent data (3.5 Å resolution):
http://rna.bgsu.edu/rna3dhub/nrlist
In the directory data/csvs, delete the default CSV file and replace with your download.
# Clone the repository and navigate to project directory
git clone https://github.com/YesselmanLab/rna_motif_library.git
cd rna_motif_library
# Create and activate new conda environment
conda create --name rna_motif_env python=3.8
conda activate rna_motif_env
# Install the package
pip install .
# Make sure you put the downloaded CSV in the right place or you will get errors
# Put the CSV where the default CSV is and delete the default
# Note: despite the use of "PDB" in language, all files are actually ".cif", not ".pdb"
# ALWAYS CLEAR THE data/out_csvs DIRECTORY BEFORE RUNNING THE SCRIPT (if it exists)! Move the data somewhere else if you want to keep it.
# If this folder is not empty (its nonexistence is OK), there will be problems!
# To create the library first we need to download the PDBs specified in the CSV
python rna_motif_library/cli.py download-cifs --threads 8
# Replace "8" with the number of CPU cores you want to use
# Estimated time: 15 minutes for around 2000 .cifs
# Expect a progress bar when it's working
# After downloading we need to process with DSSR
# need DSSR installed which is not included here
python rna_motif_library/cli.py process-dssr --threads 8
# Replace "8" with the number of CPU cores you want to use
# There will be visual feedback in the terminal window if it's working properly
# Feedback will consist of the path to the PDB/CIF files
# After processing with DSSR we need to process with SNAP
python rna_motif_library/cli.py process-snap --threads 8
# Replace "8" with the number of CPU cores you want to use
# There will be visual feedback in the terminal window if it's working properly
# Feedback will consist of the path + other information on nucleotides/etc
# After processing with SNAP we need to generate motif files
python rna_motif_library/cli.py generate-motifs
# There will be visual feedback in the terminal window if it's working properly
# Feedback will display the names of the motifs being processed