Eric Coissac
c694e1f2b0
Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
54 lines
2.1 KiB
Bash
Executable File
54 lines
2.1 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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#
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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="${SCRIPT_DIR}/stats/${TYPE}"
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case "${TYPE}" in
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indexing_presence|indexing_count)
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HEADER="run,species,strain,scatter_wall_s,scatter_rss_b,dereplicate_wall_s,dereplicate_rss_b,count_kmer_wall_s,count_kmer_rss_b,index_wall_s,index_rss_b,total_wall_s,total_rss_b"
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;;
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verify_presence)
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HEADER="run,species,strain,ref_kmers,idx_kmers,false_neg,false_pos,fn_pct,fp_pct"
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;;
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verify_count)
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HEADER="run,species,strain,ref_kmers,idx_kmers,false_neg,false_pos,count_mismatch,fn_pct,fp_pct,cm_pct"
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;;
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specific_kmer_presence|specific_kmer_count)
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HEADER="run,species,rebuild_wall_s,rebuild_rss_b,pack_wall_s,pack_rss_b,filter_total_wall_s,filter_total_rss_b,select_wall_s,select_rss_b,select_total_wall_s,select_total_rss_b"
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;;
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*)
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echo "ERROR: unknown stats type '${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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