daslab_tools

Tools, mainly for cluster usage, for Das lab at Stanford

The rna_tools was developed initially in Rosetta, but is now maintained here.

Getting started

Clone the repo to ~/src/daslab_tools, then add the following to your ~/.bashrc:

# daslab_tools — add root and all subdirectories to PATH and PYTHONPATH
export PATH="$PATH$(printf ':%s' $HOME/src/daslab_tools $HOME/src/daslab_tools/*/)"
export PYTHONPATH="$PYTHONPATH$(printf ':%s' $HOME/src/daslab_tools $HOME/src/daslab_tools/*/)"

# rna_tools subdirectories
export PATH="$PATH$(printf ':%s' $HOME/src/daslab_tools/rna_tools $HOME/src/daslab_tools/rna_tools/*/)"
export PYTHONPATH="$PYTHONPATH$(printf ':%s' $HOME/src/daslab_tools/rna_tools $HOME/src/daslab_tools/rna_tools/*/)"

Then run source ~/.bashrc. The glob */ picks up all subdirectories automatically, so no changes are needed when new subdirectories are added.

Directory structure

Directory	Contents
structure/	Structure analysis: USalign, lDDT, DSSR, OpenStructure, CIF parsing
cluster/	HPC job submission, rsync to/from cluster, Oak archival
seq/	Sequence tools: reverse complement, RNA→DNA, FASTQ/SAM utilities
data/	Data format conversion (CSV ↔ Parquet)
rna_tools/	RNA-specific tools, originally from Rosetta
rna_tools/pdb_util/	PDB structure utilities
rna_tools/silent_util/	Rosetta silent file utilities
rna_tools/cluster_setup/	Cluster job setup
rna_tools/job_setup/	Job configuration
rna_tools/cif_util/	CIF file utilities

TODO

• Update all tools to use argparse (which was not available when many of these tools were written) to more robustly handle arguments.
• Use an LLM to document all scripts.
• Provide some examples.
• Make all the pdb_tools compatible with modern CIF format and gzip.
• Fill out documentation in this README.