Compare commits
1
Commits
755cf85334
...
v1.2.3
| Author | SHA1 | Date | |
|---|---|---|---|
 Eric Coissac
|
26026288de |
+1
-19
@@ -30,25 +30,7 @@ data-stress
|
|||||||
*.bin.idx
|
*.bin.idx
|
||||||
*.prsb
|
*.prsb
|
||||||
Betula_exilis--IGA-24-33
|
Betula_exilis--IGA-24-33
|
||||||
benchmark/genomes
|
benchmark/run/
|
||||||
benchmark/genomes_orig
|
|
||||||
benchmark/simulated_data
|
|
||||||
benchmark/specimen_index_presence
|
|
||||||
benchmark/global_index_count_dense
|
|
||||||
benchmark/global_index_presence
|
|
||||||
benchmark/global_index_presence_orig
|
|
||||||
benchmark/global_index_presence_sav
|
|
||||||
benchmark/global_index_presence_dense
|
|
||||||
benchmark/all_specific
|
|
||||||
benchmark/global_index_count
|
|
||||||
benchmark/specimen_index_count
|
|
||||||
benchmark/stats
|
|
||||||
benchmark/reference_index
|
|
||||||
benchmark/reference_dist
|
|
||||||
benchmark/obikmer_dist
|
|
||||||
benchmark/specific_index_count
|
|
||||||
benchmark/specific_index_presence
|
|
||||||
benchmark/query_data
|
|
||||||
TNT
|
TNT
|
||||||
phyg
|
phyg
|
||||||
biblio
|
biblio
|
||||||
|
|||||||
+88
-83
@@ -2,23 +2,27 @@
|
|||||||
BINARY := ../src/target/release/obikmer
|
BINARY := ../src/target/release/obikmer
|
||||||
VENV_PY := ../.venv/bin/python3
|
VENV_PY := ../.venv/bin/python3
|
||||||
|
|
||||||
GENOMES := $(wildcard genomes/*.fna.gz)
|
# All generated/downloaded artifacts live under RUN/ so the whole tree can be
|
||||||
|
# gitignored with a single entry (benchmark/run/) — see benchmark/README.md.
|
||||||
|
RUN := run
|
||||||
|
|
||||||
|
GENOMES := $(wildcard $(RUN)/genomes/*.fna.gz)
|
||||||
|
|
||||||
# SPECIMENS, SPECIES, and the full dependency graph are generated by
|
# SPECIMENS, SPECIES, and the full dependency graph are generated by
|
||||||
# make_deps.py from the genome FASTA headers — like .d files in C.
|
# make_deps.py from the genome FASTA headers — like .d files in C.
|
||||||
# Make rebuilds deps.mk whenever genomes/ changes and restarts.
|
# Make rebuilds deps.mk whenever genomes/ changes and restarts.
|
||||||
-include deps.mk
|
-include deps.mk
|
||||||
|
|
||||||
REF_NPZS := $(SPECIMENS:%=reference_index/%.npz)
|
REF_NPZS := $(SPECIMENS:%=$(RUN)/reference_index/%.npz)
|
||||||
REF_DIST_CSVS := $(addprefix reference_dist/, \
|
REF_DIST_CSVS := $(addprefix $(RUN)/reference_dist/, \
|
||||||
shared_kmers.csv hamming_dist.csv jaccard_dist.csv \
|
shared_kmers.csv hamming_dist.csv jaccard_dist.csv \
|
||||||
bray_curtis_dist.csv relfreq_bray_curtis_dist.csv \
|
bray_curtis_dist.csv relfreq_bray_curtis_dist.csv \
|
||||||
euclidean_dist.csv relfreq_euclidean_dist.csv \
|
euclidean_dist.csv relfreq_euclidean_dist.csv \
|
||||||
hellinger_dist.csv hellinger_euclidean_dist.csv)
|
hellinger_dist.csv hellinger_euclidean_dist.csv)
|
||||||
OBIKMER_PRESENCE_DIST := $(addprefix obikmer_dist/presence/, \
|
OBIKMER_PRESENCE_DIST := $(addprefix $(RUN)/obikmer_dist/presence/, \
|
||||||
jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
|
jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
|
||||||
hamming_dist.csv hamming_nj.nwk)
|
hamming_dist.csv hamming_nj.nwk)
|
||||||
OBIKMER_COUNT_DIST := $(addprefix obikmer_dist/count/, \
|
OBIKMER_COUNT_DIST := $(addprefix $(RUN)/obikmer_dist/count/, \
|
||||||
jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
|
jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
|
||||||
bray_curtis_dist.csv bray_curtis_nj.nwk \
|
bray_curtis_dist.csv bray_curtis_nj.nwk \
|
||||||
relfreq_bray_curtis_dist.csv relfreq_bray_curtis_nj.nwk \
|
relfreq_bray_curtis_dist.csv relfreq_bray_curtis_nj.nwk \
|
||||||
@@ -26,28 +30,28 @@ OBIKMER_COUNT_DIST := $(addprefix obikmer_dist/count/, \
|
|||||||
relfreq_euclidean_dist.csv relfreq_euclidean_nj.nwk \
|
relfreq_euclidean_dist.csv relfreq_euclidean_nj.nwk \
|
||||||
hellinger_dist.csv hellinger_nj.nwk \
|
hellinger_dist.csv hellinger_nj.nwk \
|
||||||
hellinger_euclidean_dist.csv hellinger_euclidean_nj.nwk)
|
hellinger_euclidean_dist.csv hellinger_euclidean_nj.nwk)
|
||||||
DIST_COMPARISON := stats/dist_comparison/summary.csv
|
DIST_COMPARISON := $(RUN)/stats/dist_comparison/summary.csv
|
||||||
PRESENCE_DONE := $(SPECIMENS:%=specimen_index_presence/%/index.done)
|
PRESENCE_DONE := $(SPECIMENS:%=$(RUN)/specimen_index_presence/%/index.done)
|
||||||
PRESENCE_STATS := $(SPECIMENS:%=stats/indexing_presence/%.stats)
|
PRESENCE_STATS := $(SPECIMENS:%=$(RUN)/stats/indexing_presence/%.stats)
|
||||||
COUNT_DONE := $(SPECIMENS:%=specimen_index_count/%/index.done)
|
COUNT_DONE := $(SPECIMENS:%=$(RUN)/specimen_index_count/%/index.done)
|
||||||
COUNT_STATS := $(SPECIMENS:%=stats/indexing_count/%.stats)
|
COUNT_STATS := $(SPECIMENS:%=$(RUN)/stats/indexing_count/%.stats)
|
||||||
VERIFY_PRESENCE_STATS := $(SPECIMENS:%=stats/verify_presence/%.stats)
|
VERIFY_PRESENCE_STATS := $(SPECIMENS:%=$(RUN)/stats/verify_presence/%.stats)
|
||||||
VERIFY_COUNT_STATS := $(SPECIMENS:%=stats/verify_count/%.stats)
|
VERIFY_COUNT_STATS := $(SPECIMENS:%=$(RUN)/stats/verify_count/%.stats)
|
||||||
SPECIFIC_PRESENCE_DONE := $(SPECIES:%=specific_index_presence/%/index.done)
|
SPECIFIC_PRESENCE_DONE := $(SPECIES:%=$(RUN)/specific_index_presence/%/index.done)
|
||||||
SPECIFIC_PRESENCE_STATS := $(SPECIES:%=stats/specific_kmer_presence/%.stats)
|
SPECIFIC_PRESENCE_STATS := $(SPECIES:%=$(RUN)/stats/specific_kmer_presence/%.stats)
|
||||||
SPECIFIC_COUNT_DONE := $(SPECIES:%=specific_index_count/%/index.done)
|
SPECIFIC_COUNT_DONE := $(SPECIES:%=$(RUN)/specific_index_count/%/index.done)
|
||||||
SPECIFIC_COUNT_STATS := $(SPECIES:%=stats/specific_kmer_count/%.stats)
|
SPECIFIC_COUNT_STATS := $(SPECIES:%=$(RUN)/stats/specific_kmer_count/%.stats)
|
||||||
SIMULATED_READS := $(foreach s,$(SPECIMENS),simulated_data/$(subst --,/,$s)/reads_R1.fastq.gz)
|
SIMULATED_READS := $(foreach s,$(SPECIMENS),$(RUN)/simulated_data/$(subst --,/,$s)/reads_R1.fastq.gz)
|
||||||
QUERY_READS := $(foreach s,$(QUERY_SPECIMENS),query_data/$(subst --,/,$s)/reads_R1.fastq.gz)
|
QUERY_READS := $(foreach s,$(QUERY_SPECIMENS),$(RUN)/query_data/$(subst --,/,$s)/reads_R1.fastq.gz)
|
||||||
QUERY_PRESENCE_DENSE_DONE := $(QUERY_SPECIMENS:%=query_presence_dense/%.fasta.gz)
|
QUERY_PRESENCE_DENSE_DONE := $(QUERY_SPECIMENS:%=$(RUN)/query_presence_dense/%.fasta.gz)
|
||||||
QUERY_PRESENCE_DENSE_STATS := $(QUERY_SPECIMENS:%=stats/query_presence_dense/%.stats)
|
QUERY_PRESENCE_DENSE_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_presence_dense/%.stats)
|
||||||
QUERY_PRESENCE_SPARSE_DONE := $(QUERY_SPECIMENS:%=query_presence_sparse/%.fasta.gz)
|
QUERY_PRESENCE_SPARSE_DONE := $(QUERY_SPECIMENS:%=$(RUN)/query_presence_sparse/%.fasta.gz)
|
||||||
QUERY_PRESENCE_SPARSE_STATS := $(QUERY_SPECIMENS:%=stats/query_presence_sparse/%.stats)
|
QUERY_PRESENCE_SPARSE_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_presence_sparse/%.stats)
|
||||||
QUERY_COUNT_DENSE_DONE := $(QUERY_SPECIMENS:%=query_count_dense/%.fasta.gz)
|
QUERY_COUNT_DENSE_DONE := $(QUERY_SPECIMENS:%=$(RUN)/query_count_dense/%.fasta.gz)
|
||||||
QUERY_COUNT_DENSE_STATS := $(QUERY_SPECIMENS:%=stats/query_count_dense/%.stats)
|
QUERY_COUNT_DENSE_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_count_dense/%.stats)
|
||||||
QUERY_COUNT_SPARSE_DONE := $(QUERY_SPECIMENS:%=query_count_sparse/%.fasta.gz)
|
QUERY_COUNT_SPARSE_DONE := $(QUERY_SPECIMENS:%=$(RUN)/query_count_sparse/%.fasta.gz)
|
||||||
QUERY_COUNT_SPARSE_STATS := $(QUERY_SPECIMENS:%=stats/query_count_sparse/%.stats)
|
QUERY_COUNT_SPARSE_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_count_sparse/%.stats)
|
||||||
VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=stats/verify_query/%.stats)
|
VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/verify_query/%.stats)
|
||||||
|
|
||||||
.NOTPARALLEL:
|
.NOTPARALLEL:
|
||||||
|
|
||||||
@@ -69,8 +73,8 @@ VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=stats/verify_query/%.stats)
|
|||||||
aggregate_query_count_dense aggregate_query_count_sparse \
|
aggregate_query_count_dense aggregate_query_count_sparse \
|
||||||
verify_query aggregate_verify_query
|
verify_query aggregate_verify_query
|
||||||
|
|
||||||
verify_merge_presence: stats/verify_merge_presence/current.csv
|
verify_merge_presence: $(RUN)/stats/verify_merge_presence/current.csv
|
||||||
verify_merge_count: stats/verify_merge_count/current.csv
|
verify_merge_count: $(RUN)/stats/verify_merge_count/current.csv
|
||||||
|
|
||||||
all: aggregate_verify_presence aggregate_verify_count \
|
all: aggregate_verify_presence aggregate_verify_count \
|
||||||
verify_merge_presence verify_merge_count \
|
verify_merge_presence verify_merge_count \
|
||||||
@@ -104,7 +108,7 @@ simulate_query: $(QUERY_READS)
|
|||||||
# ── reference kmer sets ───────────────────────────────────────────────────────
|
# ── reference kmer sets ───────────────────────────────────────────────────────
|
||||||
# Prerequisites (reads → npz) are in deps.mk.
|
# Prerequisites (reads → npz) are in deps.mk.
|
||||||
|
|
||||||
reference_index/%.npz:
|
$(RUN)/reference_index/%.npz:
|
||||||
bash build_reference.sh $*
|
bash build_reference.sh $*
|
||||||
|
|
||||||
reference: $(REF_NPZS)
|
reference: $(REF_NPZS)
|
||||||
@@ -112,57 +116,58 @@ reference: $(REF_NPZS)
|
|||||||
# ── reference distance matrices ───────────────────────────────────────────────
|
# ── reference distance matrices ───────────────────────────────────────────────
|
||||||
|
|
||||||
$(REF_DIST_CSVS) &: $(REF_NPZS) build_reference_dist.py
|
$(REF_DIST_CSVS) &: $(REF_NPZS) build_reference_dist.py
|
||||||
$(VENV_PY) build_reference_dist.py
|
$(VENV_PY) build_reference_dist.py \
|
||||||
|
--ref-dir $(RUN)/reference_index --out-dir $(RUN)/reference_dist
|
||||||
|
|
||||||
reference_dist: $(REF_DIST_CSVS)
|
reference_dist: $(REF_DIST_CSVS)
|
||||||
|
|
||||||
# ── obikmer phylo (presence index) ──────────────────────────────────────────
|
# ── obikmer phylo (presence index) ──────────────────────────────────────────
|
||||||
|
|
||||||
$(OBIKMER_PRESENCE_DIST) &: global_index_presence/index.done $(BINARY)
|
$(OBIKMER_PRESENCE_DIST) &: $(RUN)/global_index_presence/index.done $(BINARY)
|
||||||
mkdir -p obikmer_dist/presence
|
mkdir -p $(RUN)/obikmer_dist/presence
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/presence/jaccard \
|
--output $(RUN)/obikmer_dist/presence/jaccard \
|
||||||
--distance jaccard --csv --shared-kmers --nj \
|
--distance jaccard --csv --shared-kmers --nj \
|
||||||
global_index_presence
|
$(RUN)/global_index_presence
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/presence/hamming \
|
--output $(RUN)/obikmer_dist/presence/hamming \
|
||||||
--distance hamming --csv --nj \
|
--distance hamming --csv --nj \
|
||||||
global_index_presence
|
$(RUN)/global_index_presence
|
||||||
|
|
||||||
obikmer_dist_presence: $(OBIKMER_PRESENCE_DIST)
|
obikmer_dist_presence: $(OBIKMER_PRESENCE_DIST)
|
||||||
|
|
||||||
# ── obikmer phylo (count index) ─────────────────────────────────────────────
|
# ── obikmer phylo (count index) ─────────────────────────────────────────────
|
||||||
|
|
||||||
$(OBIKMER_COUNT_DIST) &: global_index_count/index.done $(BINARY)
|
$(OBIKMER_COUNT_DIST) &: $(RUN)/global_index_count/index.done $(BINARY)
|
||||||
mkdir -p obikmer_dist/count
|
mkdir -p $(RUN)/obikmer_dist/count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/jaccard \
|
--output $(RUN)/obikmer_dist/count/jaccard \
|
||||||
--distance jaccard --csv --shared-kmers --nj \
|
--distance jaccard --csv --shared-kmers --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/bray_curtis \
|
--output $(RUN)/obikmer_dist/count/bray_curtis \
|
||||||
--distance bray-curtis --csv --nj \
|
--distance bray-curtis --csv --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/relfreq_bray_curtis \
|
--output $(RUN)/obikmer_dist/count/relfreq_bray_curtis \
|
||||||
--distance relfreq-bray-curtis --csv --nj \
|
--distance relfreq-bray-curtis --csv --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/euclidean \
|
--output $(RUN)/obikmer_dist/count/euclidean \
|
||||||
--distance euclidean --csv --nj \
|
--distance euclidean --csv --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/relfreq_euclidean \
|
--output $(RUN)/obikmer_dist/count/relfreq_euclidean \
|
||||||
--distance relfreq-euclidean --csv --nj \
|
--distance relfreq-euclidean --csv --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/hellinger \
|
--output $(RUN)/obikmer_dist/count/hellinger \
|
||||||
--distance hellinger --csv --nj \
|
--distance hellinger --csv --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
$(BINARY) phylo \
|
$(BINARY) phylo \
|
||||||
--output obikmer_dist/count/hellinger_euclidean \
|
--output $(RUN)/obikmer_dist/count/hellinger_euclidean \
|
||||||
--distance hellinger-euclidean --csv --nj \
|
--distance hellinger-euclidean --csv --nj \
|
||||||
global_index_count
|
$(RUN)/global_index_count
|
||||||
|
|
||||||
obikmer_dist_count: $(OBIKMER_COUNT_DIST)
|
obikmer_dist_count: $(OBIKMER_COUNT_DIST)
|
||||||
|
|
||||||
@@ -171,19 +176,19 @@ obikmer_dist: obikmer_dist_presence obikmer_dist_count
|
|||||||
# ── distance comparison ───────────────────────────────────────────────────────
|
# ── distance comparison ───────────────────────────────────────────────────────
|
||||||
|
|
||||||
$(DIST_COMPARISON): $(REF_DIST_CSVS) $(OBIKMER_PRESENCE_DIST) $(OBIKMER_COUNT_DIST) compare_all_dist.py
|
$(DIST_COMPARISON): $(REF_DIST_CSVS) $(OBIKMER_PRESENCE_DIST) $(OBIKMER_COUNT_DIST) compare_all_dist.py
|
||||||
$(VENV_PY) compare_all_dist.py --out $(DIST_COMPARISON)
|
$(VENV_PY) compare_all_dist.py --run-dir $(RUN) --out $(DIST_COMPARISON)
|
||||||
|
|
||||||
dist_comparison: $(DIST_COMPARISON)
|
dist_comparison: $(DIST_COMPARISON)
|
||||||
|
|
||||||
# ── per-specimen indexing ─────────────────────────────────────────────────────
|
# ── per-specimen indexing ─────────────────────────────────────────────────────
|
||||||
# Prerequisites (reads → index.done + .stats) are in deps.mk.
|
# Prerequisites (reads → index.done + .stats) are in deps.mk.
|
||||||
|
|
||||||
specimen_index_presence/%/index.done \
|
$(RUN)/specimen_index_presence/%/index.done \
|
||||||
stats/indexing_presence/%.stats &: $(BINARY)
|
$(RUN)/stats/indexing_presence/%.stats &: $(BINARY)
|
||||||
bash index_one_presence.sh $*
|
bash index_one_presence.sh $*
|
||||||
|
|
||||||
specimen_index_count/%/index.done \
|
$(RUN)/specimen_index_count/%/index.done \
|
||||||
stats/indexing_count/%.stats &: $(BINARY)
|
$(RUN)/stats/indexing_count/%.stats &: $(BINARY)
|
||||||
bash index_one_count.sh $*
|
bash index_one_count.sh $*
|
||||||
|
|
||||||
index_presence: $(PRESENCE_DONE)
|
index_presence: $(PRESENCE_DONE)
|
||||||
@@ -199,22 +204,22 @@ aggregate_index_count: $(COUNT_STATS)
|
|||||||
|
|
||||||
# ── global merge ──────────────────────────────────────────────────────────────
|
# ── global merge ──────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
global_index_presence/index.done: $(PRESENCE_DONE) $(BINARY)
|
$(RUN)/global_index_presence/index.done: $(PRESENCE_DONE) $(BINARY)
|
||||||
bash merge_presence.sh
|
bash merge_presence.sh
|
||||||
|
|
||||||
global_index_count/index.done: $(COUNT_DONE) $(BINARY)
|
$(RUN)/global_index_count/index.done: $(COUNT_DONE) $(BINARY)
|
||||||
bash merge_count.sh
|
bash merge_count.sh
|
||||||
|
|
||||||
merge_presence: global_index_presence/index.done
|
merge_presence: $(RUN)/global_index_presence/index.done
|
||||||
merge_count: global_index_count/index.done
|
merge_count: $(RUN)/global_index_count/index.done
|
||||||
|
|
||||||
# ── per-specimen verification ─────────────────────────────────────────────────
|
# ── per-specimen verification ─────────────────────────────────────────────────
|
||||||
# Prerequisites (index.done + npz → .stats) are in deps.mk.
|
# Prerequisites (index.done + npz → .stats) are in deps.mk.
|
||||||
|
|
||||||
stats/verify_presence/%.stats:
|
$(RUN)/stats/verify_presence/%.stats:
|
||||||
bash verify_one_presence.sh $*
|
bash verify_one_presence.sh $*
|
||||||
|
|
||||||
stats/verify_count/%.stats:
|
$(RUN)/stats/verify_count/%.stats:
|
||||||
bash verify_one_count.sh $*
|
bash verify_one_count.sh $*
|
||||||
|
|
||||||
verify_presence: $(VERIFY_PRESENCE_STATS)
|
verify_presence: $(VERIFY_PRESENCE_STATS)
|
||||||
@@ -231,12 +236,12 @@ aggregate_verify_count: $(VERIFY_COUNT_STATS)
|
|||||||
# ── species-specific indexes ──────────────────────────────────────────────────
|
# ── species-specific indexes ──────────────────────────────────────────────────
|
||||||
# Prerequisites (global index → specific index) are in deps.mk.
|
# Prerequisites (global index → specific index) are in deps.mk.
|
||||||
|
|
||||||
specific_index_presence/%/index.done \
|
$(RUN)/specific_index_presence/%/index.done \
|
||||||
stats/specific_kmer_presence/%.stats &: $(BINARY)
|
$(RUN)/stats/specific_kmer_presence/%.stats &: $(BINARY)
|
||||||
bash filter_one_presence.sh $*
|
bash filter_one_presence.sh $*
|
||||||
|
|
||||||
specific_index_count/%/index.done \
|
$(RUN)/specific_index_count/%/index.done \
|
||||||
stats/specific_kmer_count/%.stats &: $(BINARY)
|
$(RUN)/stats/specific_kmer_count/%.stats &: $(BINARY)
|
||||||
bash filter_one_count.sh $*
|
bash filter_one_count.sh $*
|
||||||
|
|
||||||
filter_presence: $(SPECIFIC_PRESENCE_DONE)
|
filter_presence: $(SPECIFIC_PRESENCE_DONE)
|
||||||
@@ -250,10 +255,10 @@ aggregate_filter_count: $(SPECIFIC_COUNT_STATS)
|
|||||||
|
|
||||||
# ── merged index verification ─────────────────────────────────────────────────
|
# ── merged index verification ─────────────────────────────────────────────────
|
||||||
|
|
||||||
stats/verify_merge_presence/current.csv: $(REF_NPZS) global_index_presence/index.done
|
$(RUN)/stats/verify_merge_presence/current.csv: $(REF_NPZS) $(RUN)/global_index_presence/index.done
|
||||||
bash verify_merge_presence.sh
|
bash verify_merge_presence.sh
|
||||||
|
|
||||||
stats/verify_merge_count/current.csv: $(REF_NPZS) global_index_count/index.done
|
$(RUN)/stats/verify_merge_count/current.csv: $(REF_NPZS) $(RUN)/global_index_count/index.done
|
||||||
bash verify_merge_count.sh
|
bash verify_merge_count.sh
|
||||||
|
|
||||||
# ── dense variants (query benchmark) ────────────────────────────────────────────
|
# ── dense variants (query benchmark) ────────────────────────────────────────────
|
||||||
@@ -262,34 +267,34 @@ stats/verify_merge_count/current.csv: $(REF_NPZS) global_index_count/index.done
|
|||||||
# built explicitly here, from a hard-link-based copy (see
|
# built explicitly here, from a hard-link-based copy (see
|
||||||
# copy_index_hardlink.sh) rather than a full `cp -r`.
|
# copy_index_hardlink.sh) rather than a full `cp -r`.
|
||||||
|
|
||||||
global_index_presence_dense/index.done: global_index_presence/index.done $(BINARY)
|
$(RUN)/global_index_presence_dense/index.done: $(RUN)/global_index_presence/index.done $(BINARY)
|
||||||
bash pack_dense.sh presence
|
bash pack_dense.sh presence
|
||||||
|
|
||||||
# Rebuilt from the per-specimen count sources directly (via `merge --dense`),
|
# Rebuilt from the per-specimen count sources directly (via `merge --dense`),
|
||||||
# not repacked from global_index_count — see pack_dense.sh's own comment.
|
# not repacked from global_index_count — see pack_dense.sh's own comment.
|
||||||
global_index_count_dense/index.done: $(COUNT_DONE) $(BINARY)
|
$(RUN)/global_index_count_dense/index.done: $(COUNT_DONE) $(BINARY)
|
||||||
bash pack_dense.sh count
|
bash pack_dense.sh count
|
||||||
|
|
||||||
pack_dense_presence: global_index_presence_dense/index.done
|
pack_dense_presence: $(RUN)/global_index_presence_dense/index.done
|
||||||
pack_dense_count: global_index_count_dense/index.done
|
pack_dense_count: $(RUN)/global_index_count_dense/index.done
|
||||||
|
|
||||||
# ── query: dense vs sparse, presence and count ──────────────────────────────────
|
# ── query: dense vs sparse, presence and count ──────────────────────────────────
|
||||||
# Prerequisites (reads + index → output + .stats) are in deps.mk.
|
# Prerequisites (reads + index → output + .stats) are in deps.mk.
|
||||||
|
|
||||||
query_presence_dense/%.fasta.gz \
|
$(RUN)/query_presence_dense/%.fasta.gz \
|
||||||
stats/query_presence_dense/%.stats &: $(BINARY) global_index_presence_dense/index.done
|
$(RUN)/stats/query_presence_dense/%.stats &: $(BINARY) $(RUN)/global_index_presence_dense/index.done
|
||||||
bash query_one.sh presence dense $*
|
bash query_one.sh presence dense $*
|
||||||
|
|
||||||
query_presence_sparse/%.fasta.gz \
|
$(RUN)/query_presence_sparse/%.fasta.gz \
|
||||||
stats/query_presence_sparse/%.stats &: $(BINARY) global_index_presence/index.done
|
$(RUN)/stats/query_presence_sparse/%.stats &: $(BINARY) $(RUN)/global_index_presence/index.done
|
||||||
bash query_one.sh presence sparse $*
|
bash query_one.sh presence sparse $*
|
||||||
|
|
||||||
query_count_dense/%.fasta.gz \
|
$(RUN)/query_count_dense/%.fasta.gz \
|
||||||
stats/query_count_dense/%.stats &: $(BINARY) global_index_count_dense/index.done
|
$(RUN)/stats/query_count_dense/%.stats &: $(BINARY) $(RUN)/global_index_count_dense/index.done
|
||||||
bash query_one.sh count dense $*
|
bash query_one.sh count dense $*
|
||||||
|
|
||||||
query_count_sparse/%.fasta.gz \
|
$(RUN)/query_count_sparse/%.fasta.gz \
|
||||||
stats/query_count_sparse/%.stats &: $(BINARY) global_index_count/index.done
|
$(RUN)/stats/query_count_sparse/%.stats &: $(BINARY) $(RUN)/global_index_count/index.done
|
||||||
bash query_one.sh count sparse $*
|
bash query_one.sh count sparse $*
|
||||||
|
|
||||||
query_presence_dense: $(QUERY_PRESENCE_DENSE_DONE)
|
query_presence_dense: $(QUERY_PRESENCE_DENSE_DONE)
|
||||||
@@ -311,7 +316,7 @@ aggregate_query_count_sparse: $(QUERY_COUNT_SPARSE_STATS)
|
|||||||
|
|
||||||
# ── query: dense/sparse regression ──────────────────────────────────────────────
|
# ── query: dense/sparse regression ──────────────────────────────────────────────
|
||||||
|
|
||||||
stats/verify_query/%.stats:
|
$(RUN)/stats/verify_query/%.stats:
|
||||||
bash verify_query_one.sh $*
|
bash verify_query_one.sh $*
|
||||||
|
|
||||||
verify_query: $(VERIFY_QUERY_STATS)
|
verify_query: $(VERIFY_QUERY_STATS)
|
||||||
|
|||||||
+108
-77
@@ -8,108 +8,124 @@ gmake simulate # simulation only
|
|||||||
gmake reference # reference kmer sets only
|
gmake reference # reference kmer sets only
|
||||||
```
|
```
|
||||||
|
|
||||||
|
All generated and downloaded artifacts live under `run/` (see
|
||||||
|
[Directory layout](#directory-layout)), so the whole tree is gitignored with
|
||||||
|
a single `benchmark/run/` entry.
|
||||||
|
|
||||||
## Pipeline overview
|
## Pipeline overview
|
||||||
|
|
||||||
```mermaid
|
```mermaid
|
||||||
flowchart TD
|
flowchart TD
|
||||||
GENOMES["genomes/*.fna.gz"]
|
GENOMES["run/genomes/*.fna.gz"]
|
||||||
BIN["obikmer binary"]
|
BIN["obikmer binary"]
|
||||||
|
|
||||||
GENOMES --> simulate
|
GENOMES --> simulate
|
||||||
simulate --> simdata[("simulated_data/")]
|
simulate --> simdata[("run/simulated_data/")]
|
||||||
|
|
||||||
simdata --> reference
|
simdata --> reference
|
||||||
reference --> refnpz[("reference_index/*.npz")]
|
reference --> refnpz[("run/reference_index/*.npz")]
|
||||||
|
|
||||||
subgraph presence ["Presence track"]
|
subgraph presence ["Presence track"]
|
||||||
simdata --> index_presence
|
simdata --> index_presence
|
||||||
BIN --> index_presence
|
BIN --> index_presence
|
||||||
index_presence --> pres_done[("specimen_index_presence/")]
|
index_presence --> pres_done[("run/specimen_index_presence/")]
|
||||||
index_presence --> pres_istats[("stats/indexing_presence/")]
|
index_presence --> pres_istats[("run/stats/indexing_presence/")]
|
||||||
pres_istats --> aggregate_index_presence
|
pres_istats --> aggregate_index_presence
|
||||||
|
|
||||||
pres_done --> merge_presence
|
pres_done --> merge_presence
|
||||||
BIN --> merge_presence
|
BIN --> merge_presence
|
||||||
merge_presence --> gpres[("global_index_presence/")]
|
merge_presence --> gpres[("run/global_index_presence/")]
|
||||||
|
|
||||||
refnpz --> verify_presence
|
refnpz --> verify_presence
|
||||||
pres_done --> verify_presence
|
pres_done --> verify_presence
|
||||||
verify_presence --> vpres_stats[("stats/verify_presence/")]
|
verify_presence --> vpres_stats[("run/stats/verify_presence/")]
|
||||||
vpres_stats --> aggregate_verify_presence
|
vpres_stats --> aggregate_verify_presence
|
||||||
|
|
||||||
gpres --> filter_presence
|
gpres --> filter_presence
|
||||||
BIN --> filter_presence
|
BIN --> filter_presence
|
||||||
filter_presence --> spec_pres[("specific_index_presence/")]
|
filter_presence --> spec_pres[("run/specific_index_presence/")]
|
||||||
filter_presence --> spec_pres_stats[("stats/specific_kmer_presence/")]
|
filter_presence --> spec_pres_stats[("run/stats/specific_kmer_presence/")]
|
||||||
spec_pres_stats --> aggregate_filter_presence
|
spec_pres_stats --> aggregate_filter_presence
|
||||||
|
|
||||||
refnpz --> verify_merge_presence
|
refnpz --> verify_merge_presence
|
||||||
gpres --> verify_merge_presence
|
gpres --> verify_merge_presence
|
||||||
verify_merge_presence --> vmp[("stats/verify_merge_presence/")]
|
verify_merge_presence --> vmp[("run/stats/verify_merge_presence/")]
|
||||||
end
|
end
|
||||||
|
|
||||||
subgraph count ["Count track"]
|
subgraph count ["Count track"]
|
||||||
simdata --> index_count
|
simdata --> index_count
|
||||||
BIN --> index_count
|
BIN --> index_count
|
||||||
index_count --> count_done[("specimen_index_count/")]
|
index_count --> count_done[("run/specimen_index_count/")]
|
||||||
index_count --> count_istats[("stats/indexing_count/")]
|
index_count --> count_istats[("run/stats/indexing_count/")]
|
||||||
count_istats --> aggregate_index_count
|
count_istats --> aggregate_index_count
|
||||||
|
|
||||||
count_done --> merge_count
|
count_done --> merge_count
|
||||||
BIN --> merge_count
|
BIN --> merge_count
|
||||||
merge_count --> gcount[("global_index_count/")]
|
merge_count --> gcount[("run/global_index_count/")]
|
||||||
|
|
||||||
refnpz --> verify_count
|
refnpz --> verify_count
|
||||||
count_done --> verify_count
|
count_done --> verify_count
|
||||||
verify_count --> vcount_stats[("stats/verify_count/")]
|
verify_count --> vcount_stats[("run/stats/verify_count/")]
|
||||||
vcount_stats --> aggregate_verify_count
|
vcount_stats --> aggregate_verify_count
|
||||||
|
|
||||||
gcount --> filter_count
|
gcount --> filter_count
|
||||||
BIN --> filter_count
|
BIN --> filter_count
|
||||||
filter_count --> spec_count[("specific_index_count/")]
|
filter_count --> spec_count[("run/specific_index_count/")]
|
||||||
filter_count --> spec_count_stats[("stats/specific_kmer_count/")]
|
filter_count --> spec_count_stats[("run/stats/specific_kmer_count/")]
|
||||||
spec_count_stats --> aggregate_filter_count
|
spec_count_stats --> aggregate_filter_count
|
||||||
|
|
||||||
refnpz --> verify_merge_count
|
refnpz --> verify_merge_count
|
||||||
gcount --> verify_merge_count
|
gcount --> verify_merge_count
|
||||||
verify_merge_count --> vmc[("stats/verify_merge_count/")]
|
verify_merge_count --> vmc[("run/stats/verify_merge_count/")]
|
||||||
end
|
end
|
||||||
|
|
||||||
subgraph query ["Query track (2 specimens: E. coli + archaeon)"]
|
subgraph query ["Query track (2 specimens: E. coli + archaeon)"]
|
||||||
GENOMES --> simulate_query
|
GENOMES --> simulate_query
|
||||||
simulate_query --> qdata[("query_data/")]
|
simulate_query --> qdata[("run/query_data/")]
|
||||||
|
|
||||||
gpres --> pack_sparse
|
gpres --> pack_dense_presence
|
||||||
BIN --> pack_sparse
|
BIN --> pack_dense_presence
|
||||||
pack_sparse --> gsparse[("global_index_presence_sparse/")]
|
pack_dense_presence --> gpresd[("run/global_index_presence_dense/")]
|
||||||
|
|
||||||
qdata --> query_dense
|
count_done --> pack_dense_count
|
||||||
gpres --> query_dense
|
BIN --> pack_dense_count
|
||||||
BIN --> query_dense
|
pack_dense_count --> gcountd[("run/global_index_count_dense/")]
|
||||||
query_dense --> qd[("query_dense/")]
|
|
||||||
query_dense --> qd_stats[("stats/query_dense/")]
|
|
||||||
qd_stats --> aggregate_query_dense
|
|
||||||
|
|
||||||
qdata --> query_sparse
|
qdata --> query_presence_dense
|
||||||
gsparse --> query_sparse
|
gpresd --> query_presence_dense
|
||||||
BIN --> query_sparse
|
query_presence_dense --> qpd[("run/query_presence_dense/")]
|
||||||
query_sparse --> qs[("query_sparse/")]
|
qpd --> aggregate_query_presence_dense
|
||||||
query_sparse --> qs_stats[("stats/query_sparse/")]
|
|
||||||
qs_stats --> aggregate_query_sparse
|
|
||||||
|
|
||||||
qd --> verify_query
|
qdata --> query_presence_sparse
|
||||||
qs --> verify_query
|
gpres --> query_presence_sparse
|
||||||
verify_query --> vq_stats[("stats/verify_query/")]
|
query_presence_sparse --> qps[("run/query_presence_sparse/")]
|
||||||
|
qps --> aggregate_query_presence_sparse
|
||||||
|
|
||||||
|
qdata --> query_count_dense
|
||||||
|
gcountd --> query_count_dense
|
||||||
|
query_count_dense --> qcd[("run/query_count_dense/")]
|
||||||
|
qcd --> aggregate_query_count_dense
|
||||||
|
|
||||||
|
qdata --> query_count_sparse
|
||||||
|
gcount --> query_count_sparse
|
||||||
|
query_count_sparse --> qcs[("run/query_count_sparse/")]
|
||||||
|
qcs --> aggregate_query_count_sparse
|
||||||
|
|
||||||
|
qpd --> verify_query
|
||||||
|
qps --> verify_query
|
||||||
|
verify_query --> vq_stats[("run/stats/verify_query/")]
|
||||||
vq_stats --> aggregate_verify_query
|
vq_stats --> aggregate_verify_query
|
||||||
end
|
end
|
||||||
|
|
||||||
aggregate_verify_presence --> all
|
aggregate_verify_presence --> all
|
||||||
aggregate_verify_count --> all
|
aggregate_verify_count --> all
|
||||||
vmp --> all
|
vmp --> all
|
||||||
vmc --> all
|
vmc --> all
|
||||||
aggregate_query_dense --> all
|
aggregate_query_presence_dense --> all
|
||||||
aggregate_query_sparse --> all
|
aggregate_query_presence_sparse --> all
|
||||||
aggregate_verify_query --> all
|
aggregate_query_count_dense --> all
|
||||||
|
aggregate_query_count_sparse --> all
|
||||||
|
aggregate_verify_query --> all
|
||||||
all -. "$(MAKE) re-eval" .-> aggregate_filter_presence
|
all -. "$(MAKE) re-eval" .-> aggregate_filter_presence
|
||||||
all -. "$(MAKE) re-eval" .-> aggregate_filter_count
|
all -. "$(MAKE) re-eval" .-> aggregate_filter_count
|
||||||
```
|
```
|
||||||
@@ -137,44 +153,59 @@ flowchart TD
|
|||||||
| `verify_merge_presence` | `verify_merge_presence.sh` | Verify global presence index against all reference sets |
|
| `verify_merge_presence` | `verify_merge_presence.sh` | Verify global presence index against all reference sets |
|
||||||
| `verify_merge_count` | `verify_merge_count.sh` | Verify global count index against all reference sets |
|
| `verify_merge_count` | `verify_merge_count.sh` | Verify global count index against all reference sets |
|
||||||
| `simulate_query` | `simulate_query_one.sh` | Simulate a fixed-size (100k pairs) read set per query specimen |
|
| `simulate_query` | `simulate_query_one.sh` | Simulate a fixed-size (100k pairs) read set per query specimen |
|
||||||
| `pack_sparse` | `pack_sparse.sh` | Build `global_index_presence_sparse/` from `global_index_presence/` |
|
| `pack_dense_presence` | `pack_dense.sh presence` | Build `global_index_presence_dense/` from `global_index_presence/` |
|
||||||
| `query_dense` | `query_one.sh dense` | Query each query specimen's reads against the dense global index |
|
| `pack_dense_count` | `pack_dense.sh count` | Build `global_index_count_dense/` from the per-specimen count sources |
|
||||||
| `query_sparse` | `query_one.sh sparse` | Query each query specimen's reads against the sparse global index |
|
| `query_presence_dense` | `query_one.sh presence dense` | Query against the dense presence global index |
|
||||||
| `aggregate_query_dense` | `aggregate_stats.sh` | Aggregate dense query wall/RSS stats |
|
| `query_presence_sparse` | `query_one.sh presence sparse` | Query against the sparse (as-merged) presence global index |
|
||||||
| `aggregate_query_sparse` | `aggregate_stats.sh` | Aggregate sparse query wall/RSS stats |
|
| `query_count_dense` | `query_one.sh count dense` | Query against the dense count global index |
|
||||||
| `verify_query` | `verify_query_one.sh` | Diff dense vs sparse query output per specimen (regression check) |
|
| `query_count_sparse` | `query_one.sh count sparse` | Query against the sparse (as-merged) count global index |
|
||||||
|
| `aggregate_query_presence_dense` | `aggregate_stats.sh` | Aggregate dense presence-query wall/RSS stats |
|
||||||
|
| `aggregate_query_presence_sparse` | `aggregate_stats.sh` | Aggregate sparse presence-query wall/RSS stats |
|
||||||
|
| `aggregate_query_count_dense` | `aggregate_stats.sh` | Aggregate dense count-query wall/RSS stats |
|
||||||
|
| `aggregate_query_count_sparse` | `aggregate_stats.sh` | Aggregate sparse count-query wall/RSS stats |
|
||||||
|
| `verify_query` | `verify_query_one.sh` | Diff dense vs sparse presence-query output per specimen (regression check) |
|
||||||
| `aggregate_verify_query` | `aggregate_stats.sh` | Aggregate dense/sparse query regression stats |
|
| `aggregate_verify_query` | `aggregate_stats.sh` | Aggregate dense/sparse query regression stats |
|
||||||
|
|
||||||
## Directory layout
|
## Directory layout
|
||||||
|
|
||||||
```
|
```
|
||||||
benchmark/
|
benchmark/
|
||||||
├── genomes/ # input reference genomes (.fna.gz)
|
└── run/ # everything generated/downloaded — gitignored as a whole
|
||||||
├── simulated_data/ # generated by simulate
|
├── genomes/ # input reference genomes (.fna.gz), downloaded by downloads.sh
|
||||||
│ └── <species>/<specimen>/
|
├── simulated_data/ # generated by simulate
|
||||||
├── query_data/ # generated by simulate_query (2 specimens, fixed 100k pairs)
|
│ └── <species>/<specimen>/
|
||||||
│ └── <species>/<specimen>/
|
├── query_data/ # generated by simulate_query (2 specimens, fixed 100k pairs)
|
||||||
├── reference_index/ # reference kmer sets (.npz)
|
│ └── <species>/<specimen>/
|
||||||
├── specimen_index_presence/ # per-specimen presence indexes
|
├── reference_index/ # reference kmer sets (.npz)
|
||||||
├── specimen_index_count/ # per-specimen count indexes
|
├── reference_dist/ # reference pairwise distance matrices
|
||||||
├── global_index_presence/ # merged global presence index (dense-packed)
|
├── obikmer_dist/ # obikmer phylo distance matrices (presence/, count/)
|
||||||
├── global_index_presence_sparse/ # global presence index, sparse-packed (query benchmark)
|
├── specimen_index_presence/ # per-specimen presence indexes
|
||||||
├── global_index_count/ # merged global count index
|
├── specimen_index_count/ # per-specimen count indexes
|
||||||
├── specific_index_presence/ # species-specific presence indexes
|
├── global_index_presence/ # merged global presence index (sparse, as merged)
|
||||||
├── specific_index_count/ # species-specific count indexes
|
├── global_index_presence_dense/ # global presence index, dense-repacked (query benchmark)
|
||||||
├── query_dense/ # query output against global_index_presence
|
├── global_index_count/ # merged global count index (sparse, as merged)
|
||||||
├── query_sparse/ # query output against global_index_presence_sparse
|
├── global_index_count_dense/ # global count index, dense-repacked (query benchmark)
|
||||||
└── stats/ # all benchmark statistics
|
├── specific_index_presence/ # species-specific presence indexes
|
||||||
├── indexing_presence/
|
├── specific_index_count/ # species-specific count indexes
|
||||||
├── indexing_count/
|
├── query_presence_dense/ # query output against global_index_presence_dense
|
||||||
├── verify_presence/
|
├── query_presence_sparse/ # query output against global_index_presence
|
||||||
├── verify_count/
|
├── query_count_dense/ # query output against global_index_count_dense
|
||||||
├── specific_kmer_presence/
|
├── query_count_sparse/ # query output against global_index_count
|
||||||
├── specific_kmer_count/
|
└── stats/ # all benchmark statistics
|
||||||
├── verify_merge_presence/
|
├── indexing_presence/
|
||||||
├── verify_merge_count/
|
├── indexing_count/
|
||||||
├── pack_sparse/
|
├── verify_presence/
|
||||||
├── query_dense/
|
├── verify_count/
|
||||||
├── query_sparse/
|
├── specific_kmer_presence/
|
||||||
└── verify_query/
|
├── specific_kmer_count/
|
||||||
|
├── verify_merge_presence/
|
||||||
|
├── verify_merge_count/
|
||||||
|
├── pack_dense_presence/
|
||||||
|
├── pack_dense_count/
|
||||||
|
├── query_presence_dense/
|
||||||
|
├── query_presence_sparse/
|
||||||
|
├── query_count_dense/
|
||||||
|
├── query_count_sparse/
|
||||||
|
├── dist_comparison/
|
||||||
|
└── verify_query/
|
||||||
```
|
```
|
||||||
|
|||||||
@@ -11,7 +11,7 @@ set -euo pipefail
|
|||||||
|
|
||||||
TYPE="$1"
|
TYPE="$1"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/${TYPE}"
|
STATS_DIR="${SCRIPT_DIR}/run/stats/${TYPE}"
|
||||||
|
|
||||||
case "${TYPE}" in
|
case "${TYPE}" in
|
||||||
indexing_presence|indexing_count)
|
indexing_presence|indexing_count)
|
||||||
|
|||||||
@@ -2,8 +2,9 @@
|
|||||||
set -euo pipefail
|
set -euo pipefail
|
||||||
|
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
SIMDATA_DIR="${SCRIPT_DIR}/simulated_data"
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
REF_DIR="${SCRIPT_DIR}/reference_index"
|
SIMDATA_DIR="${RUN_DIR}/simulated_data"
|
||||||
|
REF_DIR="${RUN_DIR}/reference_index"
|
||||||
PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
|
PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
|
||||||
BUILD_PY="${SCRIPT_DIR}/build_reference.py"
|
BUILD_PY="${SCRIPT_DIR}/build_reference.py"
|
||||||
|
|
||||||
|
|||||||
@@ -176,10 +176,10 @@ def write_csv(path: Path, labels: list[str], mat: np.ndarray, fmt: str) -> None:
|
|||||||
def main() -> None:
|
def main() -> None:
|
||||||
ap = argparse.ArgumentParser(description=__doc__,
|
ap = argparse.ArgumentParser(description=__doc__,
|
||||||
formatter_class=argparse.RawDescriptionHelpFormatter)
|
formatter_class=argparse.RawDescriptionHelpFormatter)
|
||||||
ap.add_argument('--ref-dir', default='reference_index',
|
ap.add_argument('--ref-dir', default='run/reference_index',
|
||||||
help='Directory with per-specimen .npz files (default: reference_index)')
|
help='Directory with per-specimen .npz files (default: run/reference_index)')
|
||||||
ap.add_argument('--out-dir', default='reference_dist',
|
ap.add_argument('--out-dir', default='run/reference_dist',
|
||||||
help='Output directory for CSV files (default: reference_dist)')
|
help='Output directory for CSV files (default: run/reference_dist)')
|
||||||
args = ap.parse_args()
|
args = ap.parse_args()
|
||||||
|
|
||||||
ref_dir = Path(args.ref_dir)
|
ref_dir = Path(args.ref_dir)
|
||||||
|
|||||||
@@ -150,17 +150,20 @@ def main() -> None:
|
|||||||
formatter_class=argparse.RawDescriptionHelpFormatter)
|
formatter_class=argparse.RawDescriptionHelpFormatter)
|
||||||
ap.add_argument('--tol', type=float, default=1e-4,
|
ap.add_argument('--tol', type=float, default=1e-4,
|
||||||
help='Max abs diff threshold for PASS/FAIL (default 1e-4)')
|
help='Max abs diff threshold for PASS/FAIL (default 1e-4)')
|
||||||
ap.add_argument('--out', default='stats/dist_comparison/summary.csv',
|
ap.add_argument('--run-dir', default='run',
|
||||||
|
help='Root directory holding reference_dist/ and obikmer_dist/ (default: run)')
|
||||||
|
ap.add_argument('--out', default='run/stats/dist_comparison/summary.csv',
|
||||||
help='Output summary CSV path')
|
help='Output summary CSV path')
|
||||||
args = ap.parse_args()
|
args = ap.parse_args()
|
||||||
|
|
||||||
out_path = Path(args.out)
|
out_path = Path(args.out)
|
||||||
out_path.parent.mkdir(parents=True, exist_ok=True)
|
out_path.parent.mkdir(parents=True, exist_ok=True)
|
||||||
|
|
||||||
|
run_dir = Path(args.run_dir)
|
||||||
print(f'Comparing {len(COMPARISONS)} matrix pairs…', file=sys.stderr)
|
print(f'Comparing {len(COMPARISONS)} matrix pairs…', file=sys.stderr)
|
||||||
rows = []
|
rows = []
|
||||||
for label, ref, obi in COMPARISONS:
|
for label, ref, obi in COMPARISONS:
|
||||||
rows.append(compare(label, Path(ref), Path(obi), tol=args.tol))
|
rows.append(compare(label, run_dir / ref, run_dir / obi, tol=args.tol))
|
||||||
|
|
||||||
fields = ['comparison', 'max_abs', 'mean_abs', 'rmse', 'n_pairs', 'status']
|
fields = ['comparison', 'max_abs', 'mean_abs', 'rmse', 'n_pairs', 'status']
|
||||||
with out_path.open('w', newline='') as fh:
|
with out_path.open('w', newline='') as fh:
|
||||||
|
|||||||
+152
-152
@@ -2,212 +2,212 @@ SPECIMENS := Escherichia_coli--K-12_MG1655 Escherichia_coli--EDL933 Salmonella_e
|
|||||||
SPECIES := Escherichia_coli Salmonella_enterica Bacillus_subtilis Shouchella_clausii Klebsiella_pneumoniae Opitutus_terrae Saccharolobus_islandicus Acidobacterium_capsulatum Proteus_mirabilis Wolbachia_endosymbiont Yersinia_ruckeri Candidozyma_auris
|
SPECIES := Escherichia_coli Salmonella_enterica Bacillus_subtilis Shouchella_clausii Klebsiella_pneumoniae Opitutus_terrae Saccharolobus_islandicus Acidobacterium_capsulatum Proteus_mirabilis Wolbachia_endosymbiont Yersinia_ruckeri Candidozyma_auris
|
||||||
|
|
||||||
# Escherichia_coli--K-12_MG1655
|
# Escherichia_coli--K-12_MG1655
|
||||||
simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
|
run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: run/genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
|
||||||
reference_index/Escherichia_coli--K-12_MG1655.npz: simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
|
run/reference_index/Escherichia_coli--K-12_MG1655.npz: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done stats/indexing_presence/Escherichia_coli--K-12_MG1655.stats: simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
|
run/specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done run/stats/indexing_presence/Escherichia_coli--K-12_MG1655.stats: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
|
||||||
specimen_index_count/Escherichia_coli--K-12_MG1655/index.done stats/indexing_count/Escherichia_coli--K-12_MG1655.stats: simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
|
run/specimen_index_count/Escherichia_coli--K-12_MG1655/index.done run/stats/indexing_count/Escherichia_coli--K-12_MG1655.stats: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Escherichia_coli--K-12_MG1655.stats: reference_index/Escherichia_coli--K-12_MG1655.npz specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done
|
run/stats/verify_presence/Escherichia_coli--K-12_MG1655.stats: run/reference_index/Escherichia_coli--K-12_MG1655.npz run/specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done
|
||||||
stats/verify_count/Escherichia_coli--K-12_MG1655.stats: reference_index/Escherichia_coli--K-12_MG1655.npz specimen_index_count/Escherichia_coli--K-12_MG1655/index.done
|
run/stats/verify_count/Escherichia_coli--K-12_MG1655.stats: run/reference_index/Escherichia_coli--K-12_MG1655.npz run/specimen_index_count/Escherichia_coli--K-12_MG1655/index.done
|
||||||
|
|
||||||
# Escherichia_coli--EDL933
|
# Escherichia_coli--EDL933
|
||||||
simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz: genomes/GCF_000006665.1_ASM666v1_genomic.fna.gz
|
run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz: run/genomes/GCF_000006665.1_ASM666v1_genomic.fna.gz
|
||||||
reference_index/Escherichia_coli--EDL933.npz: simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
|
run/reference_index/Escherichia_coli--EDL933.npz: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Escherichia_coli--EDL933/index.done stats/indexing_presence/Escherichia_coli--EDL933.stats: simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
|
run/specimen_index_presence/Escherichia_coli--EDL933/index.done run/stats/indexing_presence/Escherichia_coli--EDL933.stats: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
|
||||||
specimen_index_count/Escherichia_coli--EDL933/index.done stats/indexing_count/Escherichia_coli--EDL933.stats: simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
|
run/specimen_index_count/Escherichia_coli--EDL933/index.done run/stats/indexing_count/Escherichia_coli--EDL933.stats: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Escherichia_coli--EDL933.stats: reference_index/Escherichia_coli--EDL933.npz specimen_index_presence/Escherichia_coli--EDL933/index.done
|
run/stats/verify_presence/Escherichia_coli--EDL933.stats: run/reference_index/Escherichia_coli--EDL933.npz run/specimen_index_presence/Escherichia_coli--EDL933/index.done
|
||||||
stats/verify_count/Escherichia_coli--EDL933.stats: reference_index/Escherichia_coli--EDL933.npz specimen_index_count/Escherichia_coli--EDL933/index.done
|
run/stats/verify_count/Escherichia_coli--EDL933.stats: run/reference_index/Escherichia_coli--EDL933.npz run/specimen_index_count/Escherichia_coli--EDL933/index.done
|
||||||
|
|
||||||
# Salmonella_enterica--LT2
|
# Salmonella_enterica--LT2
|
||||||
simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz: genomes/GCF_000006945.2_ASM694v2_genomic.fna.gz
|
run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz: run/genomes/GCF_000006945.2_ASM694v2_genomic.fna.gz
|
||||||
reference_index/Salmonella_enterica--LT2.npz: simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
|
run/reference_index/Salmonella_enterica--LT2.npz: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Salmonella_enterica--LT2/index.done stats/indexing_presence/Salmonella_enterica--LT2.stats: simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
|
run/specimen_index_presence/Salmonella_enterica--LT2/index.done run/stats/indexing_presence/Salmonella_enterica--LT2.stats: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
|
||||||
specimen_index_count/Salmonella_enterica--LT2/index.done stats/indexing_count/Salmonella_enterica--LT2.stats: simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
|
run/specimen_index_count/Salmonella_enterica--LT2/index.done run/stats/indexing_count/Salmonella_enterica--LT2.stats: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Salmonella_enterica--LT2.stats: reference_index/Salmonella_enterica--LT2.npz specimen_index_presence/Salmonella_enterica--LT2/index.done
|
run/stats/verify_presence/Salmonella_enterica--LT2.stats: run/reference_index/Salmonella_enterica--LT2.npz run/specimen_index_presence/Salmonella_enterica--LT2/index.done
|
||||||
stats/verify_count/Salmonella_enterica--LT2.stats: reference_index/Salmonella_enterica--LT2.npz specimen_index_count/Salmonella_enterica--LT2/index.done
|
run/stats/verify_count/Salmonella_enterica--LT2.stats: run/reference_index/Salmonella_enterica--LT2.npz run/specimen_index_count/Salmonella_enterica--LT2/index.done
|
||||||
|
|
||||||
# Escherichia_coli--CFT073
|
# Escherichia_coli--CFT073
|
||||||
simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz: genomes/GCF_000007445.1_ASM744v1_genomic.fna.gz
|
run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz: run/genomes/GCF_000007445.1_ASM744v1_genomic.fna.gz
|
||||||
reference_index/Escherichia_coli--CFT073.npz: simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
|
run/reference_index/Escherichia_coli--CFT073.npz: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Escherichia_coli--CFT073/index.done stats/indexing_presence/Escherichia_coli--CFT073.stats: simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
|
run/specimen_index_presence/Escherichia_coli--CFT073/index.done run/stats/indexing_presence/Escherichia_coli--CFT073.stats: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
|
||||||
specimen_index_count/Escherichia_coli--CFT073/index.done stats/indexing_count/Escherichia_coli--CFT073.stats: simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
|
run/specimen_index_count/Escherichia_coli--CFT073/index.done run/stats/indexing_count/Escherichia_coli--CFT073.stats: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Escherichia_coli--CFT073.stats: reference_index/Escherichia_coli--CFT073.npz specimen_index_presence/Escherichia_coli--CFT073/index.done
|
run/stats/verify_presence/Escherichia_coli--CFT073.stats: run/reference_index/Escherichia_coli--CFT073.npz run/specimen_index_presence/Escherichia_coli--CFT073/index.done
|
||||||
stats/verify_count/Escherichia_coli--CFT073.stats: reference_index/Escherichia_coli--CFT073.npz specimen_index_count/Escherichia_coli--CFT073/index.done
|
run/stats/verify_count/Escherichia_coli--CFT073.stats: run/reference_index/Escherichia_coli--CFT073.npz run/specimen_index_count/Escherichia_coli--CFT073/index.done
|
||||||
|
|
||||||
# Bacillus_subtilis--168
|
# Bacillus_subtilis--168
|
||||||
simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz: genomes/GCF_000009045.1_ASM904v1_genomic.fna.gz
|
run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz: run/genomes/GCF_000009045.1_ASM904v1_genomic.fna.gz
|
||||||
reference_index/Bacillus_subtilis--168.npz: simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
|
run/reference_index/Bacillus_subtilis--168.npz: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Bacillus_subtilis--168/index.done stats/indexing_presence/Bacillus_subtilis--168.stats: simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
|
run/specimen_index_presence/Bacillus_subtilis--168/index.done run/stats/indexing_presence/Bacillus_subtilis--168.stats: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
|
||||||
specimen_index_count/Bacillus_subtilis--168/index.done stats/indexing_count/Bacillus_subtilis--168.stats: simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
|
run/specimen_index_count/Bacillus_subtilis--168/index.done run/stats/indexing_count/Bacillus_subtilis--168.stats: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Bacillus_subtilis--168.stats: reference_index/Bacillus_subtilis--168.npz specimen_index_presence/Bacillus_subtilis--168/index.done
|
run/stats/verify_presence/Bacillus_subtilis--168.stats: run/reference_index/Bacillus_subtilis--168.npz run/specimen_index_presence/Bacillus_subtilis--168/index.done
|
||||||
stats/verify_count/Bacillus_subtilis--168.stats: reference_index/Bacillus_subtilis--168.npz specimen_index_count/Bacillus_subtilis--168/index.done
|
run/stats/verify_count/Bacillus_subtilis--168.stats: run/reference_index/Bacillus_subtilis--168.npz run/specimen_index_count/Bacillus_subtilis--168/index.done
|
||||||
|
|
||||||
# Salmonella_enterica--P125109
|
# Salmonella_enterica--P125109
|
||||||
simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz: genomes/GCF_000009505.1_ASM950v1_genomic.fna.gz
|
run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz: run/genomes/GCF_000009505.1_ASM950v1_genomic.fna.gz
|
||||||
reference_index/Salmonella_enterica--P125109.npz: simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
|
run/reference_index/Salmonella_enterica--P125109.npz: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Salmonella_enterica--P125109/index.done stats/indexing_presence/Salmonella_enterica--P125109.stats: simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
|
run/specimen_index_presence/Salmonella_enterica--P125109/index.done run/stats/indexing_presence/Salmonella_enterica--P125109.stats: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
|
||||||
specimen_index_count/Salmonella_enterica--P125109/index.done stats/indexing_count/Salmonella_enterica--P125109.stats: simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
|
run/specimen_index_count/Salmonella_enterica--P125109/index.done run/stats/indexing_count/Salmonella_enterica--P125109.stats: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Salmonella_enterica--P125109.stats: reference_index/Salmonella_enterica--P125109.npz specimen_index_presence/Salmonella_enterica--P125109/index.done
|
run/stats/verify_presence/Salmonella_enterica--P125109.stats: run/reference_index/Salmonella_enterica--P125109.npz run/specimen_index_presence/Salmonella_enterica--P125109/index.done
|
||||||
stats/verify_count/Salmonella_enterica--P125109.stats: reference_index/Salmonella_enterica--P125109.npz specimen_index_count/Salmonella_enterica--P125109/index.done
|
run/stats/verify_count/Salmonella_enterica--P125109.stats: run/reference_index/Salmonella_enterica--P125109.npz run/specimen_index_count/Salmonella_enterica--P125109/index.done
|
||||||
|
|
||||||
# Shouchella_clausii--KSM-K16
|
# Shouchella_clausii--KSM-K16
|
||||||
simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz: genomes/GCF_000009825.1_ASM982v1_genomic.fna.gz
|
run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz: run/genomes/GCF_000009825.1_ASM982v1_genomic.fna.gz
|
||||||
reference_index/Shouchella_clausii--KSM-K16.npz: simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
|
run/reference_index/Shouchella_clausii--KSM-K16.npz: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Shouchella_clausii--KSM-K16/index.done stats/indexing_presence/Shouchella_clausii--KSM-K16.stats: simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
|
run/specimen_index_presence/Shouchella_clausii--KSM-K16/index.done run/stats/indexing_presence/Shouchella_clausii--KSM-K16.stats: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
|
||||||
specimen_index_count/Shouchella_clausii--KSM-K16/index.done stats/indexing_count/Shouchella_clausii--KSM-K16.stats: simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
|
run/specimen_index_count/Shouchella_clausii--KSM-K16/index.done run/stats/indexing_count/Shouchella_clausii--KSM-K16.stats: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Shouchella_clausii--KSM-K16.stats: reference_index/Shouchella_clausii--KSM-K16.npz specimen_index_presence/Shouchella_clausii--KSM-K16/index.done
|
run/stats/verify_presence/Shouchella_clausii--KSM-K16.stats: run/reference_index/Shouchella_clausii--KSM-K16.npz run/specimen_index_presence/Shouchella_clausii--KSM-K16/index.done
|
||||||
stats/verify_count/Shouchella_clausii--KSM-K16.stats: reference_index/Shouchella_clausii--KSM-K16.npz specimen_index_count/Shouchella_clausii--KSM-K16/index.done
|
run/stats/verify_count/Shouchella_clausii--KSM-K16.stats: run/reference_index/Shouchella_clausii--KSM-K16.npz run/specimen_index_count/Shouchella_clausii--KSM-K16/index.done
|
||||||
|
|
||||||
# Escherichia_coli--K-12_W3110
|
# Escherichia_coli--K-12_W3110
|
||||||
simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz: genomes/GCF_000010245.2_ASM1024v1_genomic.fna.gz
|
run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz: run/genomes/GCF_000010245.2_ASM1024v1_genomic.fna.gz
|
||||||
reference_index/Escherichia_coli--K-12_W3110.npz: simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
|
run/reference_index/Escherichia_coli--K-12_W3110.npz: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Escherichia_coli--K-12_W3110/index.done stats/indexing_presence/Escherichia_coli--K-12_W3110.stats: simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
|
run/specimen_index_presence/Escherichia_coli--K-12_W3110/index.done run/stats/indexing_presence/Escherichia_coli--K-12_W3110.stats: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
|
||||||
specimen_index_count/Escherichia_coli--K-12_W3110/index.done stats/indexing_count/Escherichia_coli--K-12_W3110.stats: simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
|
run/specimen_index_count/Escherichia_coli--K-12_W3110/index.done run/stats/indexing_count/Escherichia_coli--K-12_W3110.stats: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Escherichia_coli--K-12_W3110.stats: reference_index/Escherichia_coli--K-12_W3110.npz specimen_index_presence/Escherichia_coli--K-12_W3110/index.done
|
run/stats/verify_presence/Escherichia_coli--K-12_W3110.stats: run/reference_index/Escherichia_coli--K-12_W3110.npz run/specimen_index_presence/Escherichia_coli--K-12_W3110/index.done
|
||||||
stats/verify_count/Escherichia_coli--K-12_W3110.stats: reference_index/Escherichia_coli--K-12_W3110.npz specimen_index_count/Escherichia_coli--K-12_W3110/index.done
|
run/stats/verify_count/Escherichia_coli--K-12_W3110.stats: run/reference_index/Escherichia_coli--K-12_W3110.npz run/specimen_index_count/Escherichia_coli--K-12_W3110/index.done
|
||||||
|
|
||||||
# Klebsiella_pneumoniae--MGH_78578
|
# Klebsiella_pneumoniae--MGH_78578
|
||||||
simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz: genomes/GCF_000016305.1_ASM1630v1_genomic.fna.gz
|
run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz: run/genomes/GCF_000016305.1_ASM1630v1_genomic.fna.gz
|
||||||
reference_index/Klebsiella_pneumoniae--MGH_78578.npz: simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
|
run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done stats/indexing_presence/Klebsiella_pneumoniae--MGH_78578.stats: simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
|
run/specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--MGH_78578.stats: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
|
||||||
specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done stats/indexing_count/Klebsiella_pneumoniae--MGH_78578.stats: simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
|
run/specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done run/stats/indexing_count/Klebsiella_pneumoniae--MGH_78578.stats: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Klebsiella_pneumoniae--MGH_78578.stats: reference_index/Klebsiella_pneumoniae--MGH_78578.npz specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done
|
run/stats/verify_presence/Klebsiella_pneumoniae--MGH_78578.stats: run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz run/specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done
|
||||||
stats/verify_count/Klebsiella_pneumoniae--MGH_78578.stats: reference_index/Klebsiella_pneumoniae--MGH_78578.npz specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done
|
run/stats/verify_count/Klebsiella_pneumoniae--MGH_78578.stats: run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz run/specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done
|
||||||
|
|
||||||
# Opitutus_terrae--PB90-1
|
# Opitutus_terrae--PB90-1
|
||||||
simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz: genomes/GCF_000019965.1_ASM1996v1_genomic.fna.gz
|
run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz: run/genomes/GCF_000019965.1_ASM1996v1_genomic.fna.gz
|
||||||
reference_index/Opitutus_terrae--PB90-1.npz: simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
|
run/reference_index/Opitutus_terrae--PB90-1.npz: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Opitutus_terrae--PB90-1/index.done stats/indexing_presence/Opitutus_terrae--PB90-1.stats: simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
|
run/specimen_index_presence/Opitutus_terrae--PB90-1/index.done run/stats/indexing_presence/Opitutus_terrae--PB90-1.stats: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
|
||||||
specimen_index_count/Opitutus_terrae--PB90-1/index.done stats/indexing_count/Opitutus_terrae--PB90-1.stats: simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
|
run/specimen_index_count/Opitutus_terrae--PB90-1/index.done run/stats/indexing_count/Opitutus_terrae--PB90-1.stats: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Opitutus_terrae--PB90-1.stats: reference_index/Opitutus_terrae--PB90-1.npz specimen_index_presence/Opitutus_terrae--PB90-1/index.done
|
run/stats/verify_presence/Opitutus_terrae--PB90-1.stats: run/reference_index/Opitutus_terrae--PB90-1.npz run/specimen_index_presence/Opitutus_terrae--PB90-1/index.done
|
||||||
stats/verify_count/Opitutus_terrae--PB90-1.stats: reference_index/Opitutus_terrae--PB90-1.npz specimen_index_count/Opitutus_terrae--PB90-1/index.done
|
run/stats/verify_count/Opitutus_terrae--PB90-1.stats: run/reference_index/Opitutus_terrae--PB90-1.npz run/specimen_index_count/Opitutus_terrae--PB90-1/index.done
|
||||||
|
|
||||||
# Saccharolobus_islandicus--M.16.4
|
# Saccharolobus_islandicus--M.16.4
|
||||||
simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
|
run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: run/genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
|
||||||
reference_index/Saccharolobus_islandicus--M.16.4.npz: simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
|
run/reference_index/Saccharolobus_islandicus--M.16.4.npz: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done stats/indexing_presence/Saccharolobus_islandicus--M.16.4.stats: simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
|
run/specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done run/stats/indexing_presence/Saccharolobus_islandicus--M.16.4.stats: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
|
||||||
specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done stats/indexing_count/Saccharolobus_islandicus--M.16.4.stats: simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
|
run/specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done run/stats/indexing_count/Saccharolobus_islandicus--M.16.4.stats: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Saccharolobus_islandicus--M.16.4.stats: reference_index/Saccharolobus_islandicus--M.16.4.npz specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done
|
run/stats/verify_presence/Saccharolobus_islandicus--M.16.4.stats: run/reference_index/Saccharolobus_islandicus--M.16.4.npz run/specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done
|
||||||
stats/verify_count/Saccharolobus_islandicus--M.16.4.stats: reference_index/Saccharolobus_islandicus--M.16.4.npz specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done
|
run/stats/verify_count/Saccharolobus_islandicus--M.16.4.stats: run/reference_index/Saccharolobus_islandicus--M.16.4.npz run/specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done
|
||||||
|
|
||||||
# Acidobacterium_capsulatum--ATCC_51196
|
# Acidobacterium_capsulatum--ATCC_51196
|
||||||
simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz: genomes/GCF_000022565.1_ASM2256v1_genomic.fna.gz
|
run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz: run/genomes/GCF_000022565.1_ASM2256v1_genomic.fna.gz
|
||||||
reference_index/Acidobacterium_capsulatum--ATCC_51196.npz: simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
|
run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done stats/indexing_presence/Acidobacterium_capsulatum--ATCC_51196.stats: simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
|
run/specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done run/stats/indexing_presence/Acidobacterium_capsulatum--ATCC_51196.stats: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
|
||||||
specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done stats/indexing_count/Acidobacterium_capsulatum--ATCC_51196.stats: simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
|
run/specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done run/stats/indexing_count/Acidobacterium_capsulatum--ATCC_51196.stats: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Acidobacterium_capsulatum--ATCC_51196.stats: reference_index/Acidobacterium_capsulatum--ATCC_51196.npz specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done
|
run/stats/verify_presence/Acidobacterium_capsulatum--ATCC_51196.stats: run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz run/specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done
|
||||||
stats/verify_count/Acidobacterium_capsulatum--ATCC_51196.stats: reference_index/Acidobacterium_capsulatum--ATCC_51196.npz specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done
|
run/stats/verify_count/Acidobacterium_capsulatum--ATCC_51196.stats: run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz run/specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done
|
||||||
|
|
||||||
# Salmonella_enterica--AKU_12601
|
# Salmonella_enterica--AKU_12601
|
||||||
simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz: genomes/GCF_000026565.1_ASM2656v1_genomic.fna.gz
|
run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz: run/genomes/GCF_000026565.1_ASM2656v1_genomic.fna.gz
|
||||||
reference_index/Salmonella_enterica--AKU_12601.npz: simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
|
run/reference_index/Salmonella_enterica--AKU_12601.npz: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Salmonella_enterica--AKU_12601/index.done stats/indexing_presence/Salmonella_enterica--AKU_12601.stats: simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
|
run/specimen_index_presence/Salmonella_enterica--AKU_12601/index.done run/stats/indexing_presence/Salmonella_enterica--AKU_12601.stats: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
|
||||||
specimen_index_count/Salmonella_enterica--AKU_12601/index.done stats/indexing_count/Salmonella_enterica--AKU_12601.stats: simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
|
run/specimen_index_count/Salmonella_enterica--AKU_12601/index.done run/stats/indexing_count/Salmonella_enterica--AKU_12601.stats: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Salmonella_enterica--AKU_12601.stats: reference_index/Salmonella_enterica--AKU_12601.npz specimen_index_presence/Salmonella_enterica--AKU_12601/index.done
|
run/stats/verify_presence/Salmonella_enterica--AKU_12601.stats: run/reference_index/Salmonella_enterica--AKU_12601.npz run/specimen_index_presence/Salmonella_enterica--AKU_12601/index.done
|
||||||
stats/verify_count/Salmonella_enterica--AKU_12601.stats: reference_index/Salmonella_enterica--AKU_12601.npz specimen_index_count/Salmonella_enterica--AKU_12601/index.done
|
run/stats/verify_count/Salmonella_enterica--AKU_12601.stats: run/reference_index/Salmonella_enterica--AKU_12601.npz run/specimen_index_count/Salmonella_enterica--AKU_12601/index.done
|
||||||
|
|
||||||
# Proteus_mirabilis--HI4320
|
# Proteus_mirabilis--HI4320
|
||||||
simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz: genomes/GCF_000069965.1_ASM6996v1_genomic.fna.gz
|
run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz: run/genomes/GCF_000069965.1_ASM6996v1_genomic.fna.gz
|
||||||
reference_index/Proteus_mirabilis--HI4320.npz: simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
|
run/reference_index/Proteus_mirabilis--HI4320.npz: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Proteus_mirabilis--HI4320/index.done stats/indexing_presence/Proteus_mirabilis--HI4320.stats: simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
|
run/specimen_index_presence/Proteus_mirabilis--HI4320/index.done run/stats/indexing_presence/Proteus_mirabilis--HI4320.stats: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
|
||||||
specimen_index_count/Proteus_mirabilis--HI4320/index.done stats/indexing_count/Proteus_mirabilis--HI4320.stats: simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
|
run/specimen_index_count/Proteus_mirabilis--HI4320/index.done run/stats/indexing_count/Proteus_mirabilis--HI4320.stats: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Proteus_mirabilis--HI4320.stats: reference_index/Proteus_mirabilis--HI4320.npz specimen_index_presence/Proteus_mirabilis--HI4320/index.done
|
run/stats/verify_presence/Proteus_mirabilis--HI4320.stats: run/reference_index/Proteus_mirabilis--HI4320.npz run/specimen_index_presence/Proteus_mirabilis--HI4320/index.done
|
||||||
stats/verify_count/Proteus_mirabilis--HI4320.stats: reference_index/Proteus_mirabilis--HI4320.npz specimen_index_count/Proteus_mirabilis--HI4320/index.done
|
run/stats/verify_count/Proteus_mirabilis--HI4320.stats: run/reference_index/Proteus_mirabilis--HI4320.npz run/specimen_index_count/Proteus_mirabilis--HI4320/index.done
|
||||||
|
|
||||||
# Salmonella_enterica--CT18
|
# Salmonella_enterica--CT18
|
||||||
simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz: genomes/GCF_000195995.1_ASM19599v1_genomic.fna.gz
|
run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz: run/genomes/GCF_000195995.1_ASM19599v1_genomic.fna.gz
|
||||||
reference_index/Salmonella_enterica--CT18.npz: simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
|
run/reference_index/Salmonella_enterica--CT18.npz: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Salmonella_enterica--CT18/index.done stats/indexing_presence/Salmonella_enterica--CT18.stats: simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
|
run/specimen_index_presence/Salmonella_enterica--CT18/index.done run/stats/indexing_presence/Salmonella_enterica--CT18.stats: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
|
||||||
specimen_index_count/Salmonella_enterica--CT18/index.done stats/indexing_count/Salmonella_enterica--CT18.stats: simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
|
run/specimen_index_count/Salmonella_enterica--CT18/index.done run/stats/indexing_count/Salmonella_enterica--CT18.stats: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Salmonella_enterica--CT18.stats: reference_index/Salmonella_enterica--CT18.npz specimen_index_presence/Salmonella_enterica--CT18/index.done
|
run/stats/verify_presence/Salmonella_enterica--CT18.stats: run/reference_index/Salmonella_enterica--CT18.npz run/specimen_index_presence/Salmonella_enterica--CT18/index.done
|
||||||
stats/verify_count/Salmonella_enterica--CT18.stats: reference_index/Salmonella_enterica--CT18.npz specimen_index_count/Salmonella_enterica--CT18/index.done
|
run/stats/verify_count/Salmonella_enterica--CT18.stats: run/reference_index/Salmonella_enterica--CT18.npz run/specimen_index_count/Salmonella_enterica--CT18/index.done
|
||||||
|
|
||||||
# Klebsiella_pneumoniae--HS11286
|
# Klebsiella_pneumoniae--HS11286
|
||||||
simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz: genomes/GCF_000240185.1_ASM24018v2_genomic.fna.gz
|
run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz: run/genomes/GCF_000240185.1_ASM24018v2_genomic.fna.gz
|
||||||
reference_index/Klebsiella_pneumoniae--HS11286.npz: simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
|
run/reference_index/Klebsiella_pneumoniae--HS11286.npz: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done stats/indexing_presence/Klebsiella_pneumoniae--HS11286.stats: simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
|
run/specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--HS11286.stats: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
|
||||||
specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done stats/indexing_count/Klebsiella_pneumoniae--HS11286.stats: simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
|
run/specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done run/stats/indexing_count/Klebsiella_pneumoniae--HS11286.stats: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Klebsiella_pneumoniae--HS11286.stats: reference_index/Klebsiella_pneumoniae--HS11286.npz specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done
|
run/stats/verify_presence/Klebsiella_pneumoniae--HS11286.stats: run/reference_index/Klebsiella_pneumoniae--HS11286.npz run/specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done
|
||||||
stats/verify_count/Klebsiella_pneumoniae--HS11286.stats: reference_index/Klebsiella_pneumoniae--HS11286.npz specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done
|
run/stats/verify_count/Klebsiella_pneumoniae--HS11286.stats: run/reference_index/Klebsiella_pneumoniae--HS11286.npz run/specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done
|
||||||
|
|
||||||
# Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1
|
# Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1
|
||||||
simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz: genomes/GCF_000306885.1_ASM30688v1_genomic.fna.gz
|
run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz: run/genomes/GCF_000306885.1_ASM30688v1_genomic.fna.gz
|
||||||
reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz: simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
|
run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done stats/indexing_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
|
run/specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done run/stats/indexing_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
|
||||||
specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done stats/indexing_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
|
run/specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done run/stats/indexing_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
|
run/stats/verify_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz run/specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
|
||||||
stats/verify_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
|
run/stats/verify_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz run/specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
|
||||||
|
|
||||||
# Klebsiella_pneumoniae--ATCC_13883
|
# Klebsiella_pneumoniae--ATCC_13883
|
||||||
simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz: genomes/GCF_000742135.1_ASM74213v1_genomic.fna.gz
|
run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz: run/genomes/GCF_000742135.1_ASM74213v1_genomic.fna.gz
|
||||||
reference_index/Klebsiella_pneumoniae--ATCC_13883.npz: simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
|
run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done stats/indexing_presence/Klebsiella_pneumoniae--ATCC_13883.stats: simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
|
run/specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--ATCC_13883.stats: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
|
||||||
specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done stats/indexing_count/Klebsiella_pneumoniae--ATCC_13883.stats: simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
|
run/specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done run/stats/indexing_count/Klebsiella_pneumoniae--ATCC_13883.stats: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Klebsiella_pneumoniae--ATCC_13883.stats: reference_index/Klebsiella_pneumoniae--ATCC_13883.npz specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done
|
run/stats/verify_presence/Klebsiella_pneumoniae--ATCC_13883.stats: run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz run/specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done
|
||||||
stats/verify_count/Klebsiella_pneumoniae--ATCC_13883.stats: reference_index/Klebsiella_pneumoniae--ATCC_13883.npz specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done
|
run/stats/verify_count/Klebsiella_pneumoniae--ATCC_13883.stats: run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz run/specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done
|
||||||
|
|
||||||
# Yersinia_ruckeri--YRB
|
# Yersinia_ruckeri--YRB
|
||||||
simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz: genomes/GCF_000834255.1_ASM83425v1_genomic.fna.gz
|
run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz: run/genomes/GCF_000834255.1_ASM83425v1_genomic.fna.gz
|
||||||
reference_index/Yersinia_ruckeri--YRB.npz: simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
|
run/reference_index/Yersinia_ruckeri--YRB.npz: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Yersinia_ruckeri--YRB/index.done stats/indexing_presence/Yersinia_ruckeri--YRB.stats: simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
|
run/specimen_index_presence/Yersinia_ruckeri--YRB/index.done run/stats/indexing_presence/Yersinia_ruckeri--YRB.stats: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
|
||||||
specimen_index_count/Yersinia_ruckeri--YRB/index.done stats/indexing_count/Yersinia_ruckeri--YRB.stats: simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
|
run/specimen_index_count/Yersinia_ruckeri--YRB/index.done run/stats/indexing_count/Yersinia_ruckeri--YRB.stats: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Yersinia_ruckeri--YRB.stats: reference_index/Yersinia_ruckeri--YRB.npz specimen_index_presence/Yersinia_ruckeri--YRB/index.done
|
run/stats/verify_presence/Yersinia_ruckeri--YRB.stats: run/reference_index/Yersinia_ruckeri--YRB.npz run/specimen_index_presence/Yersinia_ruckeri--YRB/index.done
|
||||||
stats/verify_count/Yersinia_ruckeri--YRB.stats: reference_index/Yersinia_ruckeri--YRB.npz specimen_index_count/Yersinia_ruckeri--YRB/index.done
|
run/stats/verify_count/Yersinia_ruckeri--YRB.stats: run/reference_index/Yersinia_ruckeri--YRB.npz run/specimen_index_count/Yersinia_ruckeri--YRB/index.done
|
||||||
|
|
||||||
# Candidozyma_auris--GCF_003013715.1_ASM301371v2
|
# Candidozyma_auris--GCF_003013715.1_ASM301371v2
|
||||||
simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz: genomes/GCF_003013715.1_ASM301371v2_genomic.fna.gz
|
run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz: run/genomes/GCF_003013715.1_ASM301371v2_genomic.fna.gz
|
||||||
reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz: simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
|
run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
|
||||||
specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done stats/indexing_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
|
run/specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done run/stats/indexing_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
|
||||||
specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done stats/indexing_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
|
run/specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done run/stats/indexing_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
|
||||||
stats/verify_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
|
run/stats/verify_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz run/specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
|
||||||
stats/verify_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
|
run/stats/verify_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz run/specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
|
||||||
|
|
||||||
# Escherichia_coli
|
# Escherichia_coli
|
||||||
specific_index_presence/Escherichia_coli/index.done stats/specific_kmer_presence/Escherichia_coli.stats: global_index_presence/index.done
|
run/specific_index_presence/Escherichia_coli/index.done run/stats/specific_kmer_presence/Escherichia_coli.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Escherichia_coli/index.done stats/specific_kmer_count/Escherichia_coli.stats: global_index_count/index.done
|
run/specific_index_count/Escherichia_coli/index.done run/stats/specific_kmer_count/Escherichia_coli.stats: run/global_index_count/index.done
|
||||||
# Salmonella_enterica
|
# Salmonella_enterica
|
||||||
specific_index_presence/Salmonella_enterica/index.done stats/specific_kmer_presence/Salmonella_enterica.stats: global_index_presence/index.done
|
run/specific_index_presence/Salmonella_enterica/index.done run/stats/specific_kmer_presence/Salmonella_enterica.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Salmonella_enterica/index.done stats/specific_kmer_count/Salmonella_enterica.stats: global_index_count/index.done
|
run/specific_index_count/Salmonella_enterica/index.done run/stats/specific_kmer_count/Salmonella_enterica.stats: run/global_index_count/index.done
|
||||||
# Bacillus_subtilis
|
# Bacillus_subtilis
|
||||||
specific_index_presence/Bacillus_subtilis/index.done stats/specific_kmer_presence/Bacillus_subtilis.stats: global_index_presence/index.done
|
run/specific_index_presence/Bacillus_subtilis/index.done run/stats/specific_kmer_presence/Bacillus_subtilis.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Bacillus_subtilis/index.done stats/specific_kmer_count/Bacillus_subtilis.stats: global_index_count/index.done
|
run/specific_index_count/Bacillus_subtilis/index.done run/stats/specific_kmer_count/Bacillus_subtilis.stats: run/global_index_count/index.done
|
||||||
# Shouchella_clausii
|
# Shouchella_clausii
|
||||||
specific_index_presence/Shouchella_clausii/index.done stats/specific_kmer_presence/Shouchella_clausii.stats: global_index_presence/index.done
|
run/specific_index_presence/Shouchella_clausii/index.done run/stats/specific_kmer_presence/Shouchella_clausii.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Shouchella_clausii/index.done stats/specific_kmer_count/Shouchella_clausii.stats: global_index_count/index.done
|
run/specific_index_count/Shouchella_clausii/index.done run/stats/specific_kmer_count/Shouchella_clausii.stats: run/global_index_count/index.done
|
||||||
# Klebsiella_pneumoniae
|
# Klebsiella_pneumoniae
|
||||||
specific_index_presence/Klebsiella_pneumoniae/index.done stats/specific_kmer_presence/Klebsiella_pneumoniae.stats: global_index_presence/index.done
|
run/specific_index_presence/Klebsiella_pneumoniae/index.done run/stats/specific_kmer_presence/Klebsiella_pneumoniae.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Klebsiella_pneumoniae/index.done stats/specific_kmer_count/Klebsiella_pneumoniae.stats: global_index_count/index.done
|
run/specific_index_count/Klebsiella_pneumoniae/index.done run/stats/specific_kmer_count/Klebsiella_pneumoniae.stats: run/global_index_count/index.done
|
||||||
# Opitutus_terrae
|
# Opitutus_terrae
|
||||||
specific_index_presence/Opitutus_terrae/index.done stats/specific_kmer_presence/Opitutus_terrae.stats: global_index_presence/index.done
|
run/specific_index_presence/Opitutus_terrae/index.done run/stats/specific_kmer_presence/Opitutus_terrae.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Opitutus_terrae/index.done stats/specific_kmer_count/Opitutus_terrae.stats: global_index_count/index.done
|
run/specific_index_count/Opitutus_terrae/index.done run/stats/specific_kmer_count/Opitutus_terrae.stats: run/global_index_count/index.done
|
||||||
# Saccharolobus_islandicus
|
# Saccharolobus_islandicus
|
||||||
specific_index_presence/Saccharolobus_islandicus/index.done stats/specific_kmer_presence/Saccharolobus_islandicus.stats: global_index_presence/index.done
|
run/specific_index_presence/Saccharolobus_islandicus/index.done run/stats/specific_kmer_presence/Saccharolobus_islandicus.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Saccharolobus_islandicus/index.done stats/specific_kmer_count/Saccharolobus_islandicus.stats: global_index_count/index.done
|
run/specific_index_count/Saccharolobus_islandicus/index.done run/stats/specific_kmer_count/Saccharolobus_islandicus.stats: run/global_index_count/index.done
|
||||||
# Acidobacterium_capsulatum
|
# Acidobacterium_capsulatum
|
||||||
specific_index_presence/Acidobacterium_capsulatum/index.done stats/specific_kmer_presence/Acidobacterium_capsulatum.stats: global_index_presence/index.done
|
run/specific_index_presence/Acidobacterium_capsulatum/index.done run/stats/specific_kmer_presence/Acidobacterium_capsulatum.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Acidobacterium_capsulatum/index.done stats/specific_kmer_count/Acidobacterium_capsulatum.stats: global_index_count/index.done
|
run/specific_index_count/Acidobacterium_capsulatum/index.done run/stats/specific_kmer_count/Acidobacterium_capsulatum.stats: run/global_index_count/index.done
|
||||||
# Proteus_mirabilis
|
# Proteus_mirabilis
|
||||||
specific_index_presence/Proteus_mirabilis/index.done stats/specific_kmer_presence/Proteus_mirabilis.stats: global_index_presence/index.done
|
run/specific_index_presence/Proteus_mirabilis/index.done run/stats/specific_kmer_presence/Proteus_mirabilis.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Proteus_mirabilis/index.done stats/specific_kmer_count/Proteus_mirabilis.stats: global_index_count/index.done
|
run/specific_index_count/Proteus_mirabilis/index.done run/stats/specific_kmer_count/Proteus_mirabilis.stats: run/global_index_count/index.done
|
||||||
# Wolbachia_endosymbiont
|
# Wolbachia_endosymbiont
|
||||||
specific_index_presence/Wolbachia_endosymbiont/index.done stats/specific_kmer_presence/Wolbachia_endosymbiont.stats: global_index_presence/index.done
|
run/specific_index_presence/Wolbachia_endosymbiont/index.done run/stats/specific_kmer_presence/Wolbachia_endosymbiont.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Wolbachia_endosymbiont/index.done stats/specific_kmer_count/Wolbachia_endosymbiont.stats: global_index_count/index.done
|
run/specific_index_count/Wolbachia_endosymbiont/index.done run/stats/specific_kmer_count/Wolbachia_endosymbiont.stats: run/global_index_count/index.done
|
||||||
# Yersinia_ruckeri
|
# Yersinia_ruckeri
|
||||||
specific_index_presence/Yersinia_ruckeri/index.done stats/specific_kmer_presence/Yersinia_ruckeri.stats: global_index_presence/index.done
|
run/specific_index_presence/Yersinia_ruckeri/index.done run/stats/specific_kmer_presence/Yersinia_ruckeri.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Yersinia_ruckeri/index.done stats/specific_kmer_count/Yersinia_ruckeri.stats: global_index_count/index.done
|
run/specific_index_count/Yersinia_ruckeri/index.done run/stats/specific_kmer_count/Yersinia_ruckeri.stats: run/global_index_count/index.done
|
||||||
# Candidozyma_auris
|
# Candidozyma_auris
|
||||||
specific_index_presence/Candidozyma_auris/index.done stats/specific_kmer_presence/Candidozyma_auris.stats: global_index_presence/index.done
|
run/specific_index_presence/Candidozyma_auris/index.done run/stats/specific_kmer_presence/Candidozyma_auris.stats: run/global_index_presence/index.done
|
||||||
specific_index_count/Candidozyma_auris/index.done stats/specific_kmer_count/Candidozyma_auris.stats: global_index_count/index.done
|
run/specific_index_count/Candidozyma_auris/index.done run/stats/specific_kmer_count/Candidozyma_auris.stats: run/global_index_count/index.done
|
||||||
|
|
||||||
QUERY_SPECIMENS := Escherichia_coli--K-12_MG1655 Saccharolobus_islandicus--M.16.4
|
QUERY_SPECIMENS := Escherichia_coli--K-12_MG1655 Saccharolobus_islandicus--M.16.4
|
||||||
|
|
||||||
# query: Escherichia_coli--K-12_MG1655
|
# query: Escherichia_coli--K-12_MG1655
|
||||||
query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
|
run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: run/genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
|
||||||
query_dense/Escherichia_coli--K-12_MG1655.fasta.gz stats/query_dense/Escherichia_coli--K-12_MG1655.stats: query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz global_index_presence/index.done
|
run/query_presence_dense/Escherichia_coli--K-12_MG1655.fasta.gz run/stats/query_presence_dense/Escherichia_coli--K-12_MG1655.stats: run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz run/global_index_presence_dense/index.done
|
||||||
query_sparse/Escherichia_coli--K-12_MG1655.fasta.gz stats/query_sparse/Escherichia_coli--K-12_MG1655.stats: query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz global_index_presence_sparse/index.done
|
run/query_presence_sparse/Escherichia_coli--K-12_MG1655.fasta.gz run/stats/query_presence_sparse/Escherichia_coli--K-12_MG1655.stats: run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz run/global_index_presence/index.done
|
||||||
stats/verify_query/Escherichia_coli--K-12_MG1655.stats: query_dense/Escherichia_coli--K-12_MG1655.fasta.gz query_sparse/Escherichia_coli--K-12_MG1655.fasta.gz
|
run/stats/verify_query/Escherichia_coli--K-12_MG1655.stats: run/query_presence_dense/Escherichia_coli--K-12_MG1655.fasta.gz run/query_presence_sparse/Escherichia_coli--K-12_MG1655.fasta.gz
|
||||||
|
|
||||||
# query: Saccharolobus_islandicus--M.16.4
|
# query: Saccharolobus_islandicus--M.16.4
|
||||||
query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
|
run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: run/genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
|
||||||
query_dense/Saccharolobus_islandicus--M.16.4.fasta.gz stats/query_dense/Saccharolobus_islandicus--M.16.4.stats: query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz global_index_presence/index.done
|
run/query_presence_dense/Saccharolobus_islandicus--M.16.4.fasta.gz run/stats/query_presence_dense/Saccharolobus_islandicus--M.16.4.stats: run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz run/global_index_presence_dense/index.done
|
||||||
query_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz stats/query_sparse/Saccharolobus_islandicus--M.16.4.stats: query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz global_index_presence_sparse/index.done
|
run/query_presence_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz run/stats/query_presence_sparse/Saccharolobus_islandicus--M.16.4.stats: run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz run/global_index_presence/index.done
|
||||||
stats/verify_query/Saccharolobus_islandicus--M.16.4.stats: query_dense/Saccharolobus_islandicus--M.16.4.fasta.gz query_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz
|
run/stats/verify_query/Saccharolobus_islandicus--M.16.4.stats: run/query_presence_dense/Saccharolobus_islandicus--M.16.4.fasta.gz run/query_presence_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz
|
||||||
|
|||||||
@@ -29,7 +29,10 @@ assemblies=(
|
|||||||
GCF_000834255.1
|
GCF_000834255.1
|
||||||
)
|
)
|
||||||
|
|
||||||
mkdir -p genomes
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
GENOMES_DIR="${SCRIPT_DIR}/run/genomes"
|
||||||
|
|
||||||
|
mkdir -p "${GENOMES_DIR}"
|
||||||
|
|
||||||
for acc in "${assemblies[@]}"; do
|
for acc in "${assemblies[@]}"; do
|
||||||
echo "Downloading ${acc}"
|
echo "Downloading ${acc}"
|
||||||
@@ -41,7 +44,7 @@ for acc in "${assemblies[@]}"; do
|
|||||||
unzip -q "${acc}.zip" -d "${acc}"
|
unzip -q "${acc}.zip" -d "${acc}"
|
||||||
find "${acc}" -name "*.fna" |
|
find "${acc}" -name "*.fna" |
|
||||||
while read file; do
|
while read file; do
|
||||||
obiconvert -Z ${file} >genomes/$(basename ${file}).gz
|
obiconvert -Z ${file} >"${GENOMES_DIR}/$(basename ${file}).gz"
|
||||||
done
|
done
|
||||||
|
|
||||||
rm -rf "${acc}" "${acc}.zip"
|
rm -rf "${acc}" "${acc}.zip"
|
||||||
|
|||||||
@@ -12,11 +12,12 @@ set -euo pipefail
|
|||||||
|
|
||||||
SPECIES="$1"
|
SPECIES="$1"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
|
|
||||||
SOURCE="${SCRIPT_DIR}/global_index_count"
|
SOURCE="${RUN_DIR}/global_index_count"
|
||||||
OUTPUT="${SCRIPT_DIR}/specific_index_count/${SPECIES}"
|
OUTPUT="${RUN_DIR}/specific_index_count/${SPECIES}"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/specific_kmer_count"
|
STATS_DIR="${RUN_DIR}/stats/specific_kmer_count"
|
||||||
STATS_FILE="${STATS_DIR}/${SPECIES}.stats"
|
STATS_FILE="${STATS_DIR}/${SPECIES}.stats"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|||||||
@@ -12,11 +12,12 @@ set -euo pipefail
|
|||||||
|
|
||||||
SPECIES="$1"
|
SPECIES="$1"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
|
|
||||||
SOURCE="${SCRIPT_DIR}/global_index_presence"
|
SOURCE="${RUN_DIR}/global_index_presence"
|
||||||
OUTPUT="${SCRIPT_DIR}/specific_index_presence/${SPECIES}"
|
OUTPUT="${RUN_DIR}/specific_index_presence/${SPECIES}"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/specific_kmer_presence"
|
STATS_DIR="${RUN_DIR}/stats/specific_kmer_presence"
|
||||||
STATS_FILE="${STATS_DIR}/${SPECIES}.stats"
|
STATS_FILE="${STATS_DIR}/${SPECIES}.stats"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|||||||
@@ -8,14 +8,15 @@ set -euo pipefail
|
|||||||
|
|
||||||
SPECIMEN="$1"
|
SPECIMEN="$1"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
|
|
||||||
species="${SPECIMEN%%--*}"
|
species="${SPECIMEN%%--*}"
|
||||||
strain="${SPECIMEN#*--}"
|
strain="${SPECIMEN#*--}"
|
||||||
|
|
||||||
READS_DIR="${SCRIPT_DIR}/simulated_data/${species}/${strain}"
|
READS_DIR="${RUN_DIR}/simulated_data/${species}/${strain}"
|
||||||
INDEX_PATH="${SCRIPT_DIR}/specimen_index_count/${SPECIMEN}"
|
INDEX_PATH="${RUN_DIR}/specimen_index_count/${SPECIMEN}"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/indexing_count"
|
STATS_DIR="${RUN_DIR}/stats/indexing_count"
|
||||||
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|||||||
@@ -8,14 +8,15 @@ set -euo pipefail
|
|||||||
|
|
||||||
SPECIMEN="$1"
|
SPECIMEN="$1"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
|
|
||||||
species="${SPECIMEN%%--*}"
|
species="${SPECIMEN%%--*}"
|
||||||
strain="${SPECIMEN#*--}"
|
strain="${SPECIMEN#*--}"
|
||||||
|
|
||||||
READS_DIR="${SCRIPT_DIR}/simulated_data/${species}/${strain}"
|
READS_DIR="${RUN_DIR}/simulated_data/${species}/${strain}"
|
||||||
INDEX_PATH="${SCRIPT_DIR}/specimen_index_presence/${SPECIMEN}"
|
INDEX_PATH="${RUN_DIR}/specimen_index_presence/${SPECIMEN}"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/indexing_presence"
|
STATS_DIR="${RUN_DIR}/stats/indexing_presence"
|
||||||
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|||||||
+25
-21
@@ -13,6 +13,10 @@ STOP_WORDS = {'complete', 'chromosome', 'whole', 'sequence', 'genome',
|
|||||||
'endosymbiont', 'of'}
|
'endosymbiont', 'of'}
|
||||||
STOP_PREFIXES = ('scaffold', 'contig', 'plasmid')
|
STOP_PREFIXES = ('scaffold', 'contig', 'plasmid')
|
||||||
|
|
||||||
|
# All generated paths live under RUN/ (see Makefile) so the whole tree can be
|
||||||
|
# gitignored with a single entry.
|
||||||
|
RUN = 'run'
|
||||||
|
|
||||||
# Specimens used as read sources for the query benchmark (see
|
# Specimens used as read sources for the query benchmark (see
|
||||||
# DevDocMD/implementation/benchmark_query_testing.md): one common bacterium,
|
# DevDocMD/implementation/benchmark_query_testing.md): one common bacterium,
|
||||||
# one distant lineage (the only archaeon in SPECIES).
|
# one distant lineage (the only archaeon in SPECIES).
|
||||||
@@ -80,7 +84,7 @@ def main():
|
|||||||
defn = first_definition(path)
|
defn = first_definition(path)
|
||||||
sp, st = parse_organism(defn, gcf_id)
|
sp, st = parse_organism(defn, gcf_id)
|
||||||
specimen = f'{sp}--{st}'
|
specimen = f'{sp}--{st}'
|
||||||
sim_dir = f'simulated_data/{sp}/{st}'
|
sim_dir = f'{RUN}/simulated_data/{sp}/{st}'
|
||||||
entries.append((specimen, sp, sim_dir, path))
|
entries.append((specimen, sp, sim_dir, path))
|
||||||
if sp not in species_seen:
|
if sp not in species_seen:
|
||||||
species_seen.append(sp)
|
species_seen.append(sp)
|
||||||
@@ -91,13 +95,13 @@ def main():
|
|||||||
|
|
||||||
for specimen, species, sim_dir, genome in entries:
|
for specimen, species, sim_dir, genome in entries:
|
||||||
reads = f'{sim_dir}/reads_R1.fastq.gz'
|
reads = f'{sim_dir}/reads_R1.fastq.gz'
|
||||||
p_done = f'specimen_index_presence/{specimen}/index.done'
|
p_done = f'{RUN}/specimen_index_presence/{specimen}/index.done'
|
||||||
p_stats = f'stats/indexing_presence/{specimen}.stats'
|
p_stats = f'{RUN}/stats/indexing_presence/{specimen}.stats'
|
||||||
c_done = f'specimen_index_count/{specimen}/index.done'
|
c_done = f'{RUN}/specimen_index_count/{specimen}/index.done'
|
||||||
c_stats = f'stats/indexing_count/{specimen}.stats'
|
c_stats = f'{RUN}/stats/indexing_count/{specimen}.stats'
|
||||||
ref = f'reference_index/{specimen}.npz'
|
ref = f'{RUN}/reference_index/{specimen}.npz'
|
||||||
vp = f'stats/verify_presence/{specimen}.stats'
|
vp = f'{RUN}/stats/verify_presence/{specimen}.stats'
|
||||||
vc = f'stats/verify_count/{specimen}.stats'
|
vc = f'{RUN}/stats/verify_count/{specimen}.stats'
|
||||||
|
|
||||||
print()
|
print()
|
||||||
print(f'# {specimen}')
|
print(f'# {specimen}')
|
||||||
@@ -110,13 +114,13 @@ def main():
|
|||||||
|
|
||||||
print()
|
print()
|
||||||
for sp in species_seen:
|
for sp in species_seen:
|
||||||
sp_done = f'specific_index_presence/{sp}/index.done'
|
sp_done = f'{RUN}/specific_index_presence/{sp}/index.done'
|
||||||
sp_stats = f'stats/specific_kmer_presence/{sp}.stats'
|
sp_stats = f'{RUN}/stats/specific_kmer_presence/{sp}.stats'
|
||||||
sc_done = f'specific_index_count/{sp}/index.done'
|
sc_done = f'{RUN}/specific_index_count/{sp}/index.done'
|
||||||
sc_stats = f'stats/specific_kmer_count/{sp}.stats'
|
sc_stats = f'{RUN}/stats/specific_kmer_count/{sp}.stats'
|
||||||
print(f'# {sp}')
|
print(f'# {sp}')
|
||||||
print(f'{sp_done} {sp_stats}: global_index_presence/index.done')
|
print(f'{sp_done} {sp_stats}: {RUN}/global_index_presence/index.done')
|
||||||
print(f'{sc_done} {sc_stats}: global_index_count/index.done')
|
print(f'{sc_done} {sc_stats}: {RUN}/global_index_count/index.done')
|
||||||
|
|
||||||
print()
|
print()
|
||||||
print('QUERY_SPECIMENS :=', ' '.join(QUERY_SPECIMENS))
|
print('QUERY_SPECIMENS :=', ' '.join(QUERY_SPECIMENS))
|
||||||
@@ -126,17 +130,17 @@ def main():
|
|||||||
_, species, sim_dir, genome = by_specimen[specimen]
|
_, species, sim_dir, genome = by_specimen[specimen]
|
||||||
query_dir = sim_dir.replace('simulated_data/', 'query_data/', 1)
|
query_dir = sim_dir.replace('simulated_data/', 'query_data/', 1)
|
||||||
reads = f'{query_dir}/reads_R1.fastq.gz'
|
reads = f'{query_dir}/reads_R1.fastq.gz'
|
||||||
dense_out = f'query_dense/{specimen}.fasta.gz'
|
dense_out = f'{RUN}/query_presence_dense/{specimen}.fasta.gz'
|
||||||
dense_stat = f'stats/query_dense/{specimen}.stats'
|
dense_stat = f'{RUN}/stats/query_presence_dense/{specimen}.stats'
|
||||||
sparse_out = f'query_sparse/{specimen}.fasta.gz'
|
sparse_out = f'{RUN}/query_presence_sparse/{specimen}.fasta.gz'
|
||||||
sparse_stat = f'stats/query_sparse/{specimen}.stats'
|
sparse_stat = f'{RUN}/stats/query_presence_sparse/{specimen}.stats'
|
||||||
vq_stat = f'stats/verify_query/{specimen}.stats'
|
vq_stat = f'{RUN}/stats/verify_query/{specimen}.stats'
|
||||||
|
|
||||||
print()
|
print()
|
||||||
print(f'# query: {specimen}')
|
print(f'# query: {specimen}')
|
||||||
print(f'{reads}: {genome}')
|
print(f'{reads}: {genome}')
|
||||||
print(f'{dense_out} {dense_stat}: {reads} global_index_presence/index.done')
|
print(f'{dense_out} {dense_stat}: {reads} {RUN}/global_index_presence_dense/index.done')
|
||||||
print(f'{sparse_out} {sparse_stat}: {reads} global_index_presence_sparse/index.done')
|
print(f'{sparse_out} {sparse_stat}: {reads} {RUN}/global_index_presence/index.done')
|
||||||
print(f'{vq_stat}: {dense_out} {sparse_out}')
|
print(f'{vq_stat}: {dense_out} {sparse_out}')
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@@ -2,10 +2,11 @@
|
|||||||
set -euo pipefail
|
set -euo pipefail
|
||||||
|
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
IDX_DIR="${SCRIPT_DIR}/specimen_index_count"
|
IDX_DIR="${RUN_DIR}/specimen_index_count"
|
||||||
OUTPUT="${SCRIPT_DIR}/global_index_count"
|
OUTPUT="${RUN_DIR}/global_index_count"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/merge_count"
|
STATS_DIR="${RUN_DIR}/stats/merge_count"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|
||||||
|
|||||||
@@ -2,10 +2,11 @@
|
|||||||
set -euo pipefail
|
set -euo pipefail
|
||||||
|
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
IDX_DIR="${SCRIPT_DIR}/specimen_index_presence"
|
IDX_DIR="${RUN_DIR}/specimen_index_presence"
|
||||||
OUTPUT="${SCRIPT_DIR}/global_index_presence"
|
OUTPUT="${RUN_DIR}/global_index_presence"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/merge_presence"
|
STATS_DIR="${RUN_DIR}/stats/merge_presence"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|
||||||
|
|||||||
@@ -30,10 +30,11 @@ set -euo pipefail
|
|||||||
|
|
||||||
KIND="$1"
|
KIND="$1"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
SOURCE="${SCRIPT_DIR}/global_index_${KIND}"
|
SOURCE="${RUN_DIR}/global_index_${KIND}"
|
||||||
OUTPUT="${SCRIPT_DIR}/global_index_${KIND}_dense"
|
OUTPUT="${RUN_DIR}/global_index_${KIND}_dense"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/pack_dense_${KIND}"
|
STATS_DIR="${RUN_DIR}/stats/pack_dense_${KIND}"
|
||||||
STATS_FILE="${STATS_DIR}/current.stats"
|
STATS_FILE="${STATS_DIR}/current.stats"
|
||||||
|
|
||||||
mkdir -p "${STATS_DIR}"
|
mkdir -p "${STATS_DIR}"
|
||||||
|
|||||||
@@ -14,6 +14,7 @@ KIND="$1"
|
|||||||
MODE="$2"
|
MODE="$2"
|
||||||
SPECIMEN="$3"
|
SPECIMEN="$3"
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
||||||
|
|
||||||
case "${KIND}" in
|
case "${KIND}" in
|
||||||
@@ -22,17 +23,17 @@ case "${KIND}" in
|
|||||||
esac
|
esac
|
||||||
|
|
||||||
case "${MODE}" in
|
case "${MODE}" in
|
||||||
sparse) INDEX="${SCRIPT_DIR}/global_index_${KIND}" ;;
|
sparse) INDEX="${RUN_DIR}/global_index_${KIND}" ;;
|
||||||
dense) INDEX="${SCRIPT_DIR}/global_index_${KIND}_dense" ;;
|
dense) INDEX="${RUN_DIR}/global_index_${KIND}_dense" ;;
|
||||||
*) echo "ERROR: unknown mode '${MODE}' (expected dense|sparse)" >&2; exit 1 ;;
|
*) echo "ERROR: unknown mode '${MODE}' (expected dense|sparse)" >&2; exit 1 ;;
|
||||||
esac
|
esac
|
||||||
|
|
||||||
species="${SPECIMEN%%--*}"
|
species="${SPECIMEN%%--*}"
|
||||||
strain="${SPECIMEN#*--}"
|
strain="${SPECIMEN#*--}"
|
||||||
|
|
||||||
READS_DIR="${SCRIPT_DIR}/query_data/${species}/${strain}"
|
READS_DIR="${RUN_DIR}/query_data/${species}/${strain}"
|
||||||
OUT_DIR="${SCRIPT_DIR}/query_${KIND}_${MODE}"
|
OUT_DIR="${RUN_DIR}/query_${KIND}_${MODE}"
|
||||||
STATS_DIR="${SCRIPT_DIR}/stats/query_${KIND}_${MODE}"
|
STATS_DIR="${RUN_DIR}/stats/query_${KIND}_${MODE}"
|
||||||
OUT_FILE="${OUT_DIR}/${SPECIMEN}.fasta.gz"
|
OUT_FILE="${OUT_DIR}/${SPECIMEN}.fasta.gz"
|
||||||
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
||||||
|
|
||||||
|
|||||||
@@ -4,8 +4,9 @@
|
|||||||
set -euo pipefail
|
set -euo pipefail
|
||||||
|
|
||||||
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
||||||
|
RUN_DIR="${SCRIPT_DIR}/run"
|
||||||
|
|
||||||
for genome_file in "${SCRIPT_DIR}"/genomes/*.fna.gz; do
|
for genome_file in "${RUN_DIR}"/genomes/*.fna.gz; do
|
||||||
out_dir=$("${SCRIPT_DIR}/../.venv/bin/python3" "${SCRIPT_DIR}/make_deps.py" \
|
out_dir=$("${SCRIPT_DIR}/../.venv/bin/python3" "${SCRIPT_DIR}/make_deps.py" \
|
||||||
--dir-for "${genome_file}")
|
--dir-for "${genome_file}")
|
||||||
bash "${SCRIPT_DIR}/simulate_one.sh" "${genome_file}" "${out_dir}"
|
bash "${SCRIPT_DIR}/simulate_one.sh" "${genome_file}" "${out_dir}"
|
||||||
|
|||||||
@@ -1,21 +0,0 @@
|
|||||||
genome,Candidozyma_auris--GCF_003013715.1_ASM301371v2,Acidobacterium_capsulatum--ATCC_51196,Bacillus_subtilis--168,Escherichia_coli--CFT073,Escherichia_coli--EDL933,Escherichia_coli--K-12_MG1655,Escherichia_coli--K-12_W3110,Klebsiella_pneumoniae--ATCC_13883,Klebsiella_pneumoniae--HS11286,Klebsiella_pneumoniae--MGH_78578,Opitutus_terrae--PB90-1,Proteus_mirabilis--HI4320,Saccharolobus_islandicus--M.16.4,Salmonella_enterica--AKU_12601,Salmonella_enterica--CT18,Salmonella_enterica--LT2,Salmonella_enterica--P125109,Shouchella_clausii--KSM-K16,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,Yersinia_ruckeri--YRB
|
|
||||||
Candidozyma_auris--GCF_003013715.1_ASM301371v2,0.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000
|
|
||||||
Acidobacterium_capsulatum--ATCC_51196,1.000000,0.000000,0.999981,0.999990,0.999989,0.999987,0.999987,0.999990,0.999988,0.999988,0.999994,0.999989,1.000000,0.999988,0.999987,0.999987,0.999988,0.999989,0.999991,0.999987
|
|
||||||
Bacillus_subtilis--168,1.000000,0.999981,0.000000,0.999990,0.999989,0.999989,0.999989,0.999989,0.999988,0.999986,0.999995,0.999985,0.999999,0.999988,0.999987,0.999989,0.999988,0.999778,0.999993,0.999987
|
|
||||||
Escherichia_coli--CFT073,1.000000,0.999990,0.999990,0.000000,0.825741,0.807495,0.807218,0.991156,0.996855,0.997849,0.999996,0.999633,1.000000,0.993885,0.996736,0.994148,0.993821,0.999991,0.999984,0.999291
|
|
||||||
Escherichia_coli--EDL933,1.000000,0.999989,0.999989,0.825741,0.000000,0.735107,0.734775,0.996126,0.998058,0.997908,0.999997,0.999640,1.000000,0.993993,0.997126,0.994390,0.994059,0.999991,0.999986,0.999292
|
|
||||||
Escherichia_coli--K-12_MG1655,1.000000,0.999987,0.999989,0.807495,0.735107,0.000000,0.382567,0.996190,0.997747,0.997455,0.999996,0.999604,1.000000,0.993444,0.996645,0.993773,0.993431,0.999989,0.999984,0.999174
|
|
||||||
Escherichia_coli--K-12_W3110,1.000000,0.999987,0.999989,0.807218,0.734775,0.382567,0.000000,0.996220,0.997761,0.997467,0.999995,0.999604,1.000000,0.993445,0.996669,0.993769,0.993443,0.999990,0.999985,0.999165
|
|
||||||
Klebsiella_pneumoniae--ATCC_13883,1.000000,0.999990,0.999989,0.991156,0.996126,0.996190,0.996220,0.000000,0.845220,0.840545,0.999997,0.999648,1.000000,0.996177,0.998128,0.996268,0.996052,0.999990,0.999987,0.999325
|
|
||||||
Klebsiella_pneumoniae--HS11286,1.000000,0.999988,0.999988,0.996855,0.998058,0.997747,0.997761,0.845220,0.000000,0.906475,0.999996,0.999683,1.000000,0.997724,0.995697,0.997776,0.997769,0.999989,0.999979,0.999463
|
|
||||||
Klebsiella_pneumoniae--MGH_78578,1.000000,0.999988,0.999986,0.997849,0.997908,0.997455,0.997467,0.840545,0.906475,0.000000,0.999996,0.999704,1.000000,0.997928,0.995054,0.997844,0.997868,0.999990,0.999980,0.999479
|
|
||||||
Opitutus_terrae--PB90-1,1.000000,0.999994,0.999995,0.999996,0.999997,0.999996,0.999995,0.999997,0.999996,0.999996,0.000000,0.999997,0.999998,0.999996,0.999996,0.999996,0.999995,0.999997,0.999993,0.999996
|
|
||||||
Proteus_mirabilis--HI4320,1.000000,0.999989,0.999985,0.999633,0.999640,0.999604,0.999604,0.999648,0.999683,0.999704,0.999997,0.000000,1.000000,0.999604,0.999699,0.999622,0.999613,0.999987,0.999983,0.999505
|
|
||||||
Saccharolobus_islandicus--M.16.4,1.000000,1.000000,0.999999,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,0.999998,1.000000,0.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000
|
|
||||||
Salmonella_enterica--AKU_12601,1.000000,0.999988,0.999988,0.993885,0.993993,0.993444,0.993445,0.996177,0.997724,0.997928,0.999996,0.999604,1.000000,0.000000,0.869238,0.682277,0.663383,0.999990,0.999985,0.999260
|
|
||||||
Salmonella_enterica--CT18,1.000000,0.999987,0.999987,0.996736,0.997126,0.996645,0.996669,0.998128,0.995697,0.995054,0.999996,0.999699,1.000000,0.869238,0.000000,0.890872,0.886148,0.999988,0.999976,0.999524
|
|
||||||
Salmonella_enterica--LT2,1.000000,0.999987,0.999989,0.994148,0.994390,0.993773,0.993769,0.996268,0.997776,0.997844,0.999996,0.999622,1.000000,0.682277,0.890872,0.000000,0.622606,0.999989,0.999985,0.999296
|
|
||||||
Salmonella_enterica--P125109,1.000000,0.999988,0.999988,0.993821,0.994059,0.993431,0.993443,0.996052,0.997769,0.997868,0.999995,0.999613,1.000000,0.663383,0.886148,0.622606,0.000000,0.999988,0.999983,0.999270
|
|
||||||
Shouchella_clausii--KSM-K16,1.000000,0.999989,0.999778,0.999991,0.999991,0.999989,0.999990,0.999990,0.999989,0.999990,0.999997,0.999987,1.000000,0.999990,0.999988,0.999989,0.999988,0.000000,0.999991,0.999988
|
|
||||||
Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,1.000000,0.999991,0.999993,0.999984,0.999986,0.999984,0.999985,0.999987,0.999979,0.999980,0.999993,0.999983,1.000000,0.999985,0.999976,0.999985,0.999983,0.999991,0.000000,0.999983
|
|
||||||
Yersinia_ruckeri--YRB,1.000000,0.999987,0.999987,0.999291,0.999292,0.999174,0.999165,0.999325,0.999463,0.999479,0.999996,0.999505,1.000000,0.999260,0.999524,0.999296,0.999270,0.999988,0.999983,0.000000
|
|
||||||
|
@@ -1 +0,0 @@
|
|||||||
(((((((((((Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.5000001881725941,Saccharolobus_islandicus--M.16.4:0.4999993211600824):0.0000023411501775538747,Opitutus_terrae--PB90-1:0.499997075187947):0.0000029791191795691675,(Acidobacterium_capsulatum--ATCC_51196:0.49999227771334689,(Bacillus_subtilis--168:0.49988797935621456,Shouchella_clausii--KSM-K16:0.49988984146059159):0.0001037210285571577):0.0000023959836053522034):0.0000034093646568700288,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.4999920159222422):0.000199555100890203,Proteus_mirabilis--HI4320:0.49979129185300427):0.00010103619067070024,Yersinia_ruckeri--YRB:0.4996806650749249):0.0013719139155004,(Klebsiella_pneumoniae--HS11286:0.43798845051648258,(Klebsiella_pneumoniae--ATCC_13883:0.41780293826821265,Klebsiella_pneumoniae--MGH_78578:0.42274184870836559):0.017586732339732737):0.0604124197073832):0.0006482538063555254,(Salmonella_enterica--CT18:0.43952894448143017,(Salmonella_enterica--AKU_12601:0.3357977326267918,(Salmonella_enterica--LT2:0.31203395843666389,Salmonella_enterica--P125109:0.31057217324861216):0.025729515856701136):0.10292985918524672):0.05825411485542886):0.08937928015651564,Escherichia_coli--CFT073:0.40806501650701029):0.0410131211869626,Escherichia_coli--EDL933:0.3681464750911808):0.1755112579711463,Escherichia_coli--K-12_MG1655:0.19129818036662728,Escherichia_coli--K-12_W3110:0.19126872019906239);
|
|
||||||
@@ -1,21 +0,0 @@
|
|||||||
genome,Candidozyma_auris--GCF_003013715.1_ASM301371v2,Acidobacterium_capsulatum--ATCC_51196,Bacillus_subtilis--168,Escherichia_coli--CFT073,Escherichia_coli--EDL933,Escherichia_coli--K-12_MG1655,Escherichia_coli--K-12_W3110,Klebsiella_pneumoniae--ATCC_13883,Klebsiella_pneumoniae--HS11286,Klebsiella_pneumoniae--MGH_78578,Opitutus_terrae--PB90-1,Proteus_mirabilis--HI4320,Saccharolobus_islandicus--M.16.4,Salmonella_enterica--AKU_12601,Salmonella_enterica--CT18,Salmonella_enterica--LT2,Salmonella_enterica--P125109,Shouchella_clausii--KSM-K16,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,Yersinia_ruckeri--YRB
|
|
||||||
Candidozyma_auris--GCF_003013715.1_ASM301371v2,0,0,0,0,0,0,0,0,0,0,0,0,8,0,1,0,0,0,0,3
|
|
||||||
Acidobacterium_capsulatum--ATCC_51196,0,0,203,119,128,141,140,116,109,111,78,112,0,136,109,147,134,117,55,129
|
|
||||||
Bacillus_subtilis--168,0,203,0,124,132,128,123,133,109,130,66,158,6,131,112,124,135,2393,46,124
|
|
||||||
Escherichia_coli--CFT073,0,119,124,0,1966777,1998059,1999094,117743,32029,22312,63,4225,0,74946,31918,73311,76585,113,128,7854
|
|
||||||
Escherichia_coli--EDL933,0,128,132,1966777,0,2627885,2628700,52488,20134,22064,48,4202,0,74655,28602,71244,74665,112,108,7963
|
|
||||||
Escherichia_coli--K-12_MG1655,0,141,128,1998059,2627885,0,4452541,48302,21382,24602,47,4277,0,75729,30449,73622,76778,119,111,8566
|
|
||||||
Escherichia_coli--K-12_W3110,0,140,123,1999094,2628700,4452541,0,47894,21226,24470,68,4278,0,75658,30207,73614,76583,112,108,8660
|
|
||||||
Klebsiella_pneumoniae--ATCC_13883,0,116,133,117743,52488,48302,47894,0,1416091,1477759,42,4172,0,48296,18988,48144,50416,120,106,7712
|
|
||||||
Klebsiella_pneumoniae--HS11286,0,109,109,32029,20134,21382,21226,1416091,0,644063,42,2738,0,21498,29758,21606,21376,99,102,4417
|
|
||||||
Klebsiella_pneumoniae--MGH_78578,0,111,130,22312,22064,24602,24470,1477759,644063,0,42,2614,0,19948,35067,21330,20813,97,102,4374
|
|
||||||
Opitutus_terrae--PB90-1,0,78,66,63,48,47,68,42,42,42,0,43,18,57,42,53,66,39,58,43
|
|
||||||
Proteus_mirabilis--HI4320,0,112,158,4225,4202,4277,4278,4172,2738,2614,43,0,0,4254,2481,4166,4215,131,103,4704
|
|
||||||
Saccharolobus_islandicus--M.16.4,8,0,6,0,0,0,0,0,0,0,18,0,0,0,0,0,0,0,0,0
|
|
||||||
Salmonella_enterica--AKU_12601,0,136,131,74946,74655,75729,75658,48296,21498,19948,57,4254,0,0,1047731,2857146,2951421,117,108,7643
|
|
||||||
Salmonella_enterica--CT18,1,109,112,31918,28602,30449,30207,18988,29758,35067,42,2481,0,1047731,0,917948,940297,106,106,3716
|
|
||||||
Salmonella_enterica--LT2,0,147,124,73311,71244,73622,73614,48144,21606,21330,53,4166,0,2857146,917948,0,3284800,122,108,7460
|
|
||||||
Salmonella_enterica--P125109,0,134,135,76585,74665,76778,76583,50416,21376,20813,66,4215,0,2951421,940297,3284800,0,134,124,7645
|
|
||||||
Shouchella_clausii--KSM-K16,0,117,2393,113,112,119,112,120,99,97,39,131,0,117,106,122,134,0,58,124
|
|
||||||
Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,0,55,46,128,108,111,108,106,102,102,58,103,0,108,106,108,124,58,0,96
|
|
||||||
Yersinia_ruckeri--YRB,3,129,124,7854,7963,8566,8660,7712,4417,4374,43,4704,0,7643,3716,7460,7645,124,96,0
|
|
||||||
|
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user