Eric Coissac
26026288de
Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
32 lines
942 B
Bash
Executable File
32 lines
942 B
Bash
Executable File
#!/usr/bin/env bash
|
|
# Usage: verify_one_presence.sh SPECIMEN
|
|
# SPECIMEN = "species--strain" (Make pattern stem)
|
|
# Output: stats/verify_presence/SPECIMEN.stats (one CSV data row, no header)
|
|
set -euo pipefail
|
|
|
|
SPECIMEN="$1"
|
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
|
RUN_DIR="${SCRIPT_DIR}/run"
|
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
|
PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
|
|
VERIFY_PY="${SCRIPT_DIR}/verify_presence.py"
|
|
|
|
species="${SPECIMEN%%--*}"
|
|
strain="${SPECIMEN#*--}"
|
|
|
|
REF_NPZ="${RUN_DIR}/reference_index/${SPECIMEN}.npz"
|
|
INDEX_DIR="${RUN_DIR}/specimen_index_presence/${SPECIMEN}"
|
|
STATS_DIR="${RUN_DIR}/stats/verify_presence"
|
|
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
|
|
|
mkdir -p "${STATS_DIR}"
|
|
|
|
echo "[${SPECIMEN}] verifying presence"
|
|
|
|
"${PYTHON}" "${VERIFY_PY}" \
|
|
--obikmer "${BINARY}" \
|
|
--species "${species}" \
|
|
--strain "${strain}" \
|
|
"${REF_NPZ}" "${INDEX_DIR}" \
|
|
>"${STATS_FILE}"
|