daslab_tools

Tools for the Das Lab at Stanford — cluster file transfer, structure analysis, sequence utilities, and RNA-specific PDB/silent-file processing.

The rna_tools directory was developed initially in Rosetta and is now maintained here. All scripts require Python 3 and accept --help.

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.

Tools by directory

structure/

• dssr.py — run x3dna-dssr on PDB files; prints dot-bracket secondary structure and sequence
• lddt.py — compute lDDT/ilDDT scores between a reference and one or more model structures (via OST)
• ost.py — run OST compare-structures on a reference vs. multiple PDBs
• split_models.py — split a multi-model PDB into individual numbered files
• thread_rna.py — thread a target sequence onto backbone atoms of a template PDB
• fix_o2prime.py — strip and rebuild O2′ atoms (fixes bad geometry from some structure predictors)
• USalign.py — wrapper for USalign structure superposition and TM-score

cluster/

• rsync_to_cluster.py (r2c) — rsync files from the current directory to a named cluster destination
• rsync_from_cluster.py (rfc) — rsync files from a named cluster destination to the current directory
• cd_to_cluster.py (c2c) — print the equivalent of the current directory on another filesystem
• cluster_info.py — list known destinations; cluster_info.py -a shows resolved host and path for each
• prepare_slurm.py — generate SLURM sbatch scripts from a plain-text list of commands
• archive_to_oak.py — tar a directory and copy it to Oak long-term storage
• rosetta_submit.py — submit Rosetta jobs across cluster destinations

seq/

• rc.py — reverse complement a DNA or RNA sequence
• rna2dna.py — convert an RNA sequence to DNA (U→T)
• gel_from_fastq.py — simulate a gel image from FASTQ read-length distribution
• sam_counts.py — count reads per reference sequence from a SAM file

data/

• csv_to_parquet.py — convert a CSV file to Parquet
• parquet_to_csv.py — convert a Parquet file to CSV
• clean_parquet.py — filter or clean columns in a Parquet file

rna_tools/pdb_util/

• renumber_pdb_in_place.py (rpip) — renumber residues in place; supports negative numbers and chain specs
• pdbsubset.py — extract specified residues from a PDB (by residue number, chain, or range)
• pdbslice.py — extract a contiguous range or custom subset/excision of residues
• extract_chain.py — extract one or more chains from a PDB (supports gzip)
• replace_chain.py / replace_chain_inplace.py — rename chain IDs in a PDB
• reorder_pdb.py / reorder_to_standard_pdb.py — reorder ATOM records to Rosetta or standard PDB order
• pdb2fasta.py — extract a FASTA-format sequence from a PDB
• get_sequence.py — print the residue sequence from a PDB
• get_res_num.py — list residue numbers present in a PDB
• check_cutpoints.py — identify chain cutpoints in a PDB
• make_rna_rosetta_ready.py — prepare an RNA PDB for Rosetta (renumber, strip ions, fix chains)
• fetch_pdb.py — download a PDB entry by accession code
• get_surrounding_res.py — find residues within a distance cutoff of a target residue
• rna_helix.py — build an ideal A-form RNA helix for a given sequence
• rna_mutate.py — mutate residues in an RNA PDB
• rna_thread.py — thread a new sequence onto an RNA backbone
• plot_contour.py — plot contour maps from nucleobase_sample_around score tables
• prepare_rna_puzzle_submissions.py — assemble a ranked multi-model PDB for RNA Puzzles submission

rna_tools/silent_util/

• extract_lowscore_decoys.py (ex) — extract the lowest-scoring structures from a Rosetta silent file
• extract_lowscore_decoys_outfile.py (exo) — same, writing to a named output file
• extract_lowscore_decoys_multiple_outfiles.py — extract from multiple silent files in one call
• cat_outfiles.py — concatenate Rosetta silent/out files, deduplicating SEQUENCE and description headers
• fields.py (fp) — show which column numbers correspond to which score terms
• plot_score_vs_rms.py — scatter plot of score vs. RMS from one or more Rosetta .out files
• silent_file_sort_and_select.py — sort and filter a Rosetta silent file by score

rna_tools/job_setup/

• rna_denovo_setup.py — generate Rosetta rna_denovo job scripts from sequence and secondary structure
• helix_preassemble_setup.py — set up helix pre-assembly jobs for Rosetta
• parallel_min_setup.py — set up parallel minimization jobs
• parse_tag.py / make_tag.py — parse and create Rosetta-style residue/chain tag strings
• rosetta_exe.py — locate Rosetta executables on the current system

rna_tools/cif_util/

• extract_chain_from_cif.py — extract a single chain from an mmCIF file

TODO

• Provide some examples.
• Make all the pdb_tools compatible with modern CIF format and gzip.