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.
145 lines
6.1 KiB
Makefile
145 lines
6.1 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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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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.NOTPARALLEL:
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.PHONY: all simulate reference \
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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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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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# ── dependency file ───────────────────────────────────────────────────────────
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deps.mk: $(GENOMES)
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$(VENV_PY) make_deps.py $^ > $@
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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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# ── 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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# ── 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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