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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
41 lines
1.2 KiB
Bash
Executable File
41 lines
1.2 KiB
Bash
Executable File
#!/usr/bin/env bash
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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RUN_DIR="${SCRIPT_DIR}/run"
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SIMDATA_DIR="${RUN_DIR}/simulated_data"
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REF_DIR="${RUN_DIR}/reference_index"
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PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
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BUILD_PY="${SCRIPT_DIR}/build_reference.py"
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KMER_SIZE="${KMER_SIZE:-31}"
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MIN_ABUNDANCE="${MIN_ABUNDANCE:-1}"
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mkdir -p "${REF_DIR}"
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for species_dir in "${SIMDATA_DIR}"/*/; do
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[[ -d "${species_dir}" ]] || continue
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species=$(basename "${species_dir}")
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for strain_dir in "${species_dir}"*/; do
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[[ -d "${strain_dir}" ]] || continue
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strain=$(basename "${strain_dir}")
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r1="${strain_dir}/reads_R1.fastq.gz"
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r2="${strain_dir}/reads_R2.fastq.gz"
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if [[ ! -f "${r1}" || ! -f "${r2}" ]]; then
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echo "SKIP ${species}--${strain}: reads not found" >&2
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continue
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fi
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out="${REF_DIR}/${species}--${strain}.npz"
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echo "[${species}--${strain}] → ${out}"
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"${PYTHON}" "${BUILD_PY}" \
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--kmer-size "${KMER_SIZE}" \
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--min-abundance "${MIN_ABUNDANCE}" \
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--output "${out}" \
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"${r1}" "${r2}"
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done
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done
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