29 lines
834 B
Bash
29 lines
834 B
Bash
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#!/usr/bin/env bash
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# Usage: verify_query_one.sh SPECIMEN
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# SPECIMEN = "species--strain" (Make pattern stem)
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# Output: stats/verify_query/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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PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
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VERIFY_PY="${SCRIPT_DIR}/verify_query.py"
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species="${SPECIMEN%%--*}"
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strain="${SPECIMEN#*--}"
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DENSE="${SCRIPT_DIR}/query_dense/${SPECIMEN}.fasta.gz"
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SPARSE="${SCRIPT_DIR}/query_sparse/${SPECIMEN}.fasta.gz"
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STATS_DIR="${SCRIPT_DIR}/stats/verify_query"
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STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
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mkdir -p "${STATS_DIR}"
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echo "[${SPECIMEN}] verifying query (dense vs sparse)"
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"${PYTHON}" "${VERIFY_PY}" \
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--species "${species}" \
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--strain "${strain}" \
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"${DENSE}" "${SPARSE}" \
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>"${STATS_FILE}"
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