31 lines
923 B
Bash
31 lines
923 B
Bash
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#!/usr/bin/env bash
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# Usage: verify_one_presence.sh SPECIMEN
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# SPECIMEN = "species--strain" (Make pattern stem)
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# Output: stats/verify_presence/SPECIMEN.stats (one CSV data row, no header)
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set -euo pipefail
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SPECIMEN="$1"
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
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PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
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VERIFY_PY="${SCRIPT_DIR}/verify_presence.py"
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species="${SPECIMEN%%--*}"
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strain="${SPECIMEN#*--}"
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REF_NPZ="${SCRIPT_DIR}/reference_index/${SPECIMEN}.npz"
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INDEX_DIR="${SCRIPT_DIR}/specimen_index_presence/${SPECIMEN}"
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STATS_DIR="${SCRIPT_DIR}/stats/verify_presence"
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STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
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mkdir -p "${STATS_DIR}"
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echo "[${SPECIMEN}] verifying presence"
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"${PYTHON}" "${VERIFY_PY}" \
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--obikmer "${BINARY}" \
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--species "${species}" \
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--strain "${strain}" \
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"${REF_NPZ}" "${INDEX_DIR}" \
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>"${STATS_FILE}"
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