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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
62 lines
2.5 KiB
Bash
Executable File
62 lines
2.5 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Usage: aggregate_stats.sh TYPE
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# TYPE = indexing_presence | indexing_count | verify_presence | verify_count |
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# query_presence_dense | query_presence_sparse |
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# query_count_dense | query_count_sparse
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#
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# Reads all stats/TYPE/*.stats files (one CSV data row each, no header).
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# Creates a new stats/TYPE/run_NNN.csv only if any .stats file is newer than
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# the most recent run CSV (idempotent when nothing changed).
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set -euo pipefail
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TYPE="$1"
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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STATS_DIR="${SCRIPT_DIR}/run/stats/${TYPE}"
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case "${TYPE}" in
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indexing_presence|indexing_count)
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HEADER="run,species,strain,scatter_wall_s,scatter_rss_b,dereplicate_wall_s,dereplicate_rss_b,count_kmer_wall_s,count_kmer_rss_b,index_wall_s,index_rss_b,total_wall_s,total_rss_b"
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;;
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verify_presence)
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HEADER="run,species,strain,ref_kmers,idx_kmers,false_neg,false_pos,fn_pct,fp_pct"
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;;
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verify_count)
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HEADER="run,species,strain,ref_kmers,idx_kmers,false_neg,false_pos,count_mismatch,fn_pct,fp_pct,cm_pct"
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;;
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specific_kmer_presence|specific_kmer_count)
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HEADER="run,species,rebuild_wall_s,rebuild_rss_b,pack_wall_s,pack_rss_b,filter_total_wall_s,filter_total_rss_b,select_wall_s,select_rss_b,select_total_wall_s,select_total_rss_b"
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;;
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query_presence_dense|query_presence_sparse|query_count_dense|query_count_sparse)
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HEADER="run,species,strain,query_wall_s,query_rss_b,total_wall_s,total_rss_b"
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;;
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verify_query)
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HEADER="run,species,strain,n_reads,n_common,missing_in_dense,missing_in_sparse,mismatched,mismatch_pct"
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;;
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*)
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echo "ERROR: unknown stats type '${TYPE}'" >&2
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exit 1
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;;
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esac
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# Find most recent existing run CSV (empty string if none).
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latest_csv=$(find "${STATS_DIR}" -maxdepth 1 -name 'run_*.csv' 2>/dev/null | sort | tail -1)
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# Check if any .stats file is newer than the latest run CSV.
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if [[ -n "${latest_csv}" ]] && \
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[[ -z "$(find "${STATS_DIR}" -maxdepth 1 -name '*.stats' -newer "${latest_csv}" 2>/dev/null)" ]]; then
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echo "[${TYPE}] stats up to date (${latest_csv})"
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exit 0
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fi
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run_n=$(printf '%03d' "$(find "${STATS_DIR}" -maxdepth 1 -name 'run_*.csv' 2>/dev/null | wc -l | tr -d ' ')")
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CSV="${STATS_DIR}/run_${run_n}.csv"
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echo "${HEADER}" >"${CSV}"
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# Sort .stats files by name for reproducible row order.
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while IFS= read -r stats_file; do
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sed "s/^/${run_n},/" "${stats_file}"
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done < <(find "${STATS_DIR}" -maxdepth 1 -name '*.stats' | sort) >>"${CSV}"
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echo "[${TYPE}] run ${run_n} → ${CSV}"
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