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Usage

Installation

Venv:

python3 -m venv .venv
source .venv/bin/activate
pip install -e .

From repo checkout:

./RNAcs --version

Dependencies

RNAcs --check-deps
RNAcs --check-deps --rscape
RNAcs --show-tool-paths

Basic run

RNAcs --input-alignment aln.{stk,aln} --output-dir run_dir --cores all

Common options

Override window sizes:

RNAcs --input-alignment aln.stk --maxbpspan 100 --maxbpspan 200 --cores all

Enable R-scape:

RNAcs --input-alignment aln.stk --rscape --cores all

Allow RNAz shuffling (default: disabled):

RNAcs --input-alignment aln.stk --rnaz-shuffle --cores all

Conservative output reuse (only rebuild if inputs changed):

RNAcs --input-alignment aln.stk --conservative --cores all

Output

Main results per maxbpspan:

results/versions.yaml                            # toolchain versions
generated_files/summary/len_*/RNAConSnake.log.csv        # all windows
generated_files/summary/len_*/RNAConSnake.nr.csv         # one per locus
generated_files/summary/len_*/RNAConSnake.md             # both tables
generated_files/alignment_screenability.tsv     # per-window occupancy

Calibration (with --null-arm):

results/calibration/qvalues.tsv          # per-locus q-values
results/calibration/summary.json         # FDR, method, parameters
results/calibration/funnel.tsv           # filter stages per arm

Export (with --export-bundle):

<bundle>/manifest.json                   # schema and provenance
<bundle>/candidates.csv                  # all loci with q-values

De-replication

Each run writes both full and de-replicated tables. Change method:

RNAcs --input-alignment aln.stk --dereplicate substructure --cores all

Methods: containment (default), substructure, overlap, none.

Details: dereplication.md

Alignment screenability

Every run writes where the screen is blind (too gappy, too divergent):

column -ts$'\t' generated_files/alignment_screenability.tsv | less

Or on alignment alone:

python -m rnaconsnake.tools.alignment_report --alignment aln.stk \
  --output screenability.tsv --metadata screenability.json

Null-model calibration

RNAcs --input-alignment aln.stk --null-arm sissiz \
  --null-replicates 100 --output-dir run_dir --cores all

Methods: sissiz (default), rnazRandomizeAln, none.

Reproducibility: SISSIz cannot be seeded. Pin a pool:

RNAcs --input-alignment aln.stk --null-arm sissiz \
  --null-pool /path/to/run/null_pool/pool.stk --output-dir run_dir \
  --cores all

Details: configuration_lock.md

Analysis aids

Fold and plot a span:

python -m rnaconsnake.tools.fold_region --alignment aln.stk \
  --start 100 --end 200 --output-dir review/span1 --label elem1

Sweep cascade thresholds:

python -m rnaconsnake.tools.threshold_sweep \
  --arm-input real:100:run/arms/real/generated_files/summary/len_100/RNAConSnake.log.csv \
  --arm-input null_000:100:run/arms/null_000/generated_files/summary/len_100/RNAConSnake.log.csv \
  ... one per arm ... \
  --output sweep.tsv

Measure detection floor:

python -m rnaconsnake.tools.sensitivity_envelope \
  --alignment aln_known.stk --manifest envelope/manifest.tsv \
  --output-dir envelope/subsets --sizes 3,4,5,6