Eric Coissac
89ea077456
Introduces a complete query benchmark track to evaluate performance and verify consistency between dense and sparse index formats. Adds scripts to simulate fixed-size paired-end reads, pack a sparse presence index, execute queries in both modes, and capture wall time and RSS metrics. Includes a verification step that compares outputs by read ID to ensure content identity across parallel processing. Updates build configuration, documentation, and ignore patterns to support the new pipeline for two microbial specimens.
287 lines
12 KiB
Makefile
287 lines
12 KiB
Makefile
# Requires GNU Make >= 4.3 (grouped targets &:) — use gmake on macOS
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BINARY := ../src/target/release/obikmer
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VENV_PY := ../.venv/bin/python3
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GENOMES := $(wildcard genomes/*.fna.gz)
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# SPECIMENS, SPECIES, and the full dependency graph are generated by
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# make_deps.py from the genome FASTA headers — like .d files in C.
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# Make rebuilds deps.mk whenever genomes/ changes and restarts.
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-include deps.mk
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REF_NPZS := $(SPECIMENS:%=reference_index/%.npz)
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REF_DIST_CSVS := $(addprefix reference_dist/, \
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shared_kmers.csv hamming_dist.csv jaccard_dist.csv \
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bray_curtis_dist.csv relfreq_bray_curtis_dist.csv \
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euclidean_dist.csv relfreq_euclidean_dist.csv \
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hellinger_dist.csv hellinger_euclidean_dist.csv)
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OBIKMER_PRESENCE_DIST := $(addprefix obikmer_dist/presence/, \
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jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
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hamming_dist.csv hamming_nj.nwk)
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OBIKMER_COUNT_DIST := $(addprefix obikmer_dist/count/, \
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jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
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bray_curtis_dist.csv bray_curtis_nj.nwk \
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relfreq_bray_curtis_dist.csv relfreq_bray_curtis_nj.nwk \
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euclidean_dist.csv euclidean_nj.nwk \
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relfreq_euclidean_dist.csv relfreq_euclidean_nj.nwk \
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hellinger_dist.csv hellinger_nj.nwk \
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hellinger_euclidean_dist.csv hellinger_euclidean_nj.nwk)
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DIST_COMPARISON := stats/dist_comparison/summary.csv
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PRESENCE_DONE := $(SPECIMENS:%=specimen_index_presence/%/index.done)
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PRESENCE_STATS := $(SPECIMENS:%=stats/indexing_presence/%.stats)
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COUNT_DONE := $(SPECIMENS:%=specimen_index_count/%/index.done)
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COUNT_STATS := $(SPECIMENS:%=stats/indexing_count/%.stats)
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VERIFY_PRESENCE_STATS := $(SPECIMENS:%=stats/verify_presence/%.stats)
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VERIFY_COUNT_STATS := $(SPECIMENS:%=stats/verify_count/%.stats)
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SPECIFIC_PRESENCE_DONE := $(SPECIES:%=specific_index_presence/%/index.done)
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SPECIFIC_PRESENCE_STATS := $(SPECIES:%=stats/specific_kmer_presence/%.stats)
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SPECIFIC_COUNT_DONE := $(SPECIES:%=specific_index_count/%/index.done)
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SPECIFIC_COUNT_STATS := $(SPECIES:%=stats/specific_kmer_count/%.stats)
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SIMULATED_READS := $(foreach s,$(SPECIMENS),simulated_data/$(subst --,/,$s)/reads_R1.fastq.gz)
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QUERY_READS := $(foreach s,$(QUERY_SPECIMENS),query_data/$(subst --,/,$s)/reads_R1.fastq.gz)
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QUERY_DENSE_DONE := $(QUERY_SPECIMENS:%=query_dense/%.fasta.gz)
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QUERY_DENSE_STATS := $(QUERY_SPECIMENS:%=stats/query_dense/%.stats)
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QUERY_SPARSE_DONE := $(QUERY_SPECIMENS:%=query_sparse/%.fasta.gz)
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QUERY_SPARSE_STATS := $(QUERY_SPECIMENS:%=stats/query_sparse/%.stats)
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VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=stats/verify_query/%.stats)
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.NOTPARALLEL:
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.PHONY: all simulate reference reference_dist \
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obikmer_dist obikmer_dist_presence obikmer_dist_count \
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dist_comparison \
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index_presence index_count \
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aggregate_index_presence aggregate_index_count \
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merge_presence merge_count \
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verify_presence verify_count \
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aggregate_verify_presence aggregate_verify_count \
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verify_merge_presence verify_merge_count \
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filter_presence filter_count \
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aggregate_filter_presence aggregate_filter_count \
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pack_sparse simulate_query \
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query_dense query_sparse \
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aggregate_query_dense aggregate_query_sparse \
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verify_query aggregate_verify_query
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verify_merge_presence: stats/verify_merge_presence/current.csv
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verify_merge_count: stats/verify_merge_count/current.csv
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all: aggregate_verify_presence aggregate_verify_count \
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verify_merge_presence verify_merge_count \
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aggregate_filter_presence aggregate_filter_count \
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dist_comparison \
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aggregate_query_dense aggregate_query_sparse aggregate_verify_query
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# ── dependency file ───────────────────────────────────────────────────────────
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deps.mk: $(GENOMES) make_deps.py
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$(VENV_PY) make_deps.py $(GENOMES) > $@
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# ── simulation ────────────────────────────────────────────────────────────────
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# Prerequisites (genome → reads) are in deps.mk; $< is the genome file.
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$(SIMULATED_READS):
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bash simulate_one.sh $< $(dir $@)
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simulate: $(SIMULATED_READS)
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# ── query read simulation (fixed size, independent draw) ───────────────────────
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# Prerequisites (genome → reads) are in deps.mk; $< is the genome file.
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$(QUERY_READS):
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bash simulate_query_one.sh $< $(dir $@)
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simulate_query: $(QUERY_READS)
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# ── reference kmer sets ───────────────────────────────────────────────────────
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# Prerequisites (reads → npz) are in deps.mk.
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reference_index/%.npz:
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bash build_reference.sh $*
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reference: $(REF_NPZS)
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# ── reference distance matrices ───────────────────────────────────────────────
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$(REF_DIST_CSVS) &: $(REF_NPZS) build_reference_dist.py
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$(VENV_PY) build_reference_dist.py
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reference_dist: $(REF_DIST_CSVS)
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# ── obikmer phylo (presence index) ──────────────────────────────────────────
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$(OBIKMER_PRESENCE_DIST) &: global_index_presence/index.done $(BINARY)
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mkdir -p obikmer_dist/presence
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$(BINARY) phylo \
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--output obikmer_dist/presence/jaccard \
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--metric jaccard --shared-kmers --nj \
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global_index_presence
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$(BINARY) phylo \
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--output obikmer_dist/presence/hamming \
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--metric hamming --nj \
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global_index_presence
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obikmer_dist_presence: $(OBIKMER_PRESENCE_DIST)
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# ── obikmer phylo (count index) ─────────────────────────────────────────────
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$(OBIKMER_COUNT_DIST) &: global_index_count/index.done $(BINARY)
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mkdir -p obikmer_dist/count
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$(BINARY) phylo \
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--output obikmer_dist/count/jaccard \
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--metric jaccard --shared-kmers --nj \
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global_index_count
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$(BINARY) phylo \
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--output obikmer_dist/count/bray_curtis \
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--metric bray-curtis --nj \
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global_index_count
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$(BINARY) phylo \
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--output obikmer_dist/count/relfreq_bray_curtis \
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--metric relfreq-bray-curtis --nj \
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global_index_count
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$(BINARY) phylo \
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--output obikmer_dist/count/euclidean \
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--metric euclidean --nj \
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global_index_count
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$(BINARY) phylo \
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--output obikmer_dist/count/relfreq_euclidean \
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--metric relfreq-euclidean --nj \
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global_index_count
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$(BINARY) phylo \
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--output obikmer_dist/count/hellinger \
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--metric hellinger --nj \
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global_index_count
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$(BINARY) phylo \
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--output obikmer_dist/count/hellinger_euclidean \
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--metric hellinger-euclidean --nj \
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global_index_count
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obikmer_dist_count: $(OBIKMER_COUNT_DIST)
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obikmer_dist: obikmer_dist_presence obikmer_dist_count
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# ── distance comparison ───────────────────────────────────────────────────────
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$(DIST_COMPARISON): $(REF_DIST_CSVS) $(OBIKMER_PRESENCE_DIST) $(OBIKMER_COUNT_DIST) compare_all_dist.py
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$(VENV_PY) compare_all_dist.py --out $(DIST_COMPARISON)
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dist_comparison: $(DIST_COMPARISON)
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# ── per-specimen indexing ─────────────────────────────────────────────────────
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# Prerequisites (reads → index.done + .stats) are in deps.mk.
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specimen_index_presence/%/index.done \
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stats/indexing_presence/%.stats &: $(BINARY)
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bash index_one_presence.sh $*
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specimen_index_count/%/index.done \
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stats/indexing_count/%.stats &: $(BINARY)
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bash index_one_count.sh $*
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index_presence: $(PRESENCE_DONE)
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index_count: $(COUNT_DONE)
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# ── indexing stats aggregation ────────────────────────────────────────────────
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aggregate_index_presence: $(PRESENCE_STATS)
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bash aggregate_stats.sh indexing_presence
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aggregate_index_count: $(COUNT_STATS)
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bash aggregate_stats.sh indexing_count
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# ── global merge ──────────────────────────────────────────────────────────────
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global_index_presence/index.done: $(PRESENCE_DONE) $(BINARY)
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bash merge_presence.sh
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global_index_count/index.done: $(COUNT_DONE) $(BINARY)
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bash merge_count.sh
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merge_presence: global_index_presence/index.done
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merge_count: global_index_count/index.done
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# ── per-specimen verification ─────────────────────────────────────────────────
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# Prerequisites (index.done + npz → .stats) are in deps.mk.
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stats/verify_presence/%.stats:
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bash verify_one_presence.sh $*
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stats/verify_count/%.stats:
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bash verify_one_count.sh $*
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verify_presence: $(VERIFY_PRESENCE_STATS)
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verify_count: $(VERIFY_COUNT_STATS)
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# ── verification stats aggregation ───────────────────────────────────────────
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aggregate_verify_presence: $(VERIFY_PRESENCE_STATS)
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bash aggregate_stats.sh verify_presence
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aggregate_verify_count: $(VERIFY_COUNT_STATS)
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bash aggregate_stats.sh verify_count
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# ── species-specific indexes ──────────────────────────────────────────────────
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# Prerequisites (global index → specific index) are in deps.mk.
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specific_index_presence/%/index.done \
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stats/specific_kmer_presence/%.stats &: $(BINARY)
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bash filter_one_presence.sh $*
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specific_index_count/%/index.done \
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stats/specific_kmer_count/%.stats &: $(BINARY)
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bash filter_one_count.sh $*
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filter_presence: $(SPECIFIC_PRESENCE_DONE)
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filter_count: $(SPECIFIC_COUNT_DONE)
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aggregate_filter_presence: $(SPECIFIC_PRESENCE_STATS)
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bash aggregate_stats.sh specific_kmer_presence
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aggregate_filter_count: $(SPECIFIC_COUNT_STATS)
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bash aggregate_stats.sh specific_kmer_count
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# ── merged index verification ─────────────────────────────────────────────────
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stats/verify_merge_presence/current.csv: $(REF_NPZS) global_index_presence/index.done
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bash verify_merge_presence.sh
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stats/verify_merge_count/current.csv: $(REF_NPZS) global_index_count/index.done
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bash verify_merge_count.sh
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# ── sparse presence index (query benchmark) ─────────────────────────────────────
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global_index_presence_sparse/index.done: global_index_presence/index.done $(BINARY)
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bash pack_sparse.sh
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pack_sparse: global_index_presence_sparse/index.done
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# ── query: dense vs sparse ───────────────────────────────────────────────────────
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# Prerequisites (reads + index → output + .stats) are in deps.mk.
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query_dense/%.fasta.gz \
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stats/query_dense/%.stats &: $(BINARY)
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bash query_one.sh dense $*
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query_sparse/%.fasta.gz \
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stats/query_sparse/%.stats &: $(BINARY)
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bash query_one.sh sparse $*
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query_dense: $(QUERY_DENSE_DONE)
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query_sparse: $(QUERY_SPARSE_DONE)
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aggregate_query_dense: $(QUERY_DENSE_STATS)
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bash aggregate_stats.sh query_dense
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aggregate_query_sparse: $(QUERY_SPARSE_STATS)
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bash aggregate_stats.sh query_sparse
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# ── query: dense/sparse regression ──────────────────────────────────────────────
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stats/verify_query/%.stats:
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bash verify_query_one.sh $*
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verify_query: $(VERIFY_QUERY_STATS)
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aggregate_verify_query: $(VERIFY_QUERY_STATS)
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bash aggregate_stats.sh verify_query
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