40 lines
1.2 KiB
Bash
40 lines
1.2 KiB
Bash
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#!/usr/bin/env bash
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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SIMDATA_DIR="${SCRIPT_DIR}/simulated_data"
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REF_DIR="${SCRIPT_DIR}/reference_index"
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PYTHON="${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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