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Makefile
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EMAIL=$(shell git config user.email)
DATA=data
BUILD=build
SCRIPTS=$(DATA)/scripts
GO_VERSION=2024-01-17
GO_OBO=$(DATA)/ontologies/go$(GO_VERSION).obo
MIBIG=$(DATA)/mibig
MIBIG_VERSION=3.1
INTERPRO_VERSION=98.0
INTERPRO_XML=$(DATA)/pfam/interpro$(INTERPRO_VERSION).xml.gz
INTERPRO_JSON=$(DATA)/pfam/interpro$(INTERPRO_VERSION).json
PFAM_VERSION=36.0
PFAM_HMM=$(DATA)/pfam/Pfam$(PFAM_VERSION).hmm
ATLAS=$(DATA)/npatlas/NPAtlas_download.json.gz
CHEMONT=$(DATA)/ontologies/ChemOnt_2_1.obo
DATASET_NAMES=mibig3.1 mibig2.0
DATASET_TABLES=features classes ani
TAXONOMY=$(DATA)/taxonomy
TAXONOMY_VERSION=2023-06-01
PYTHON=python -Wignore
WGET=wget --no-check-certificate
# use http://classyfire.wishartlab.com/ to get ClassyFire annotations
WISHART=--wishart
.PHONY: datasets
datasets: features classes compounds clusters maccs
.PHONY: features
features: $(foreach dataset,$(DATASET_NAMES),$(DATA)/datasets/$(dataset)/features.hdf5)
.PHONY: classes
classes: $(foreach dataset,$(DATASET_NAMES),$(DATA)/datasets/$(dataset)/classes.hdf5)
.PHONY: maccs
maccs: $(foreach dataset,$(DATASET_NAMES),$(DATA)/datasets/$(dataset)/maccs.hdf5)
.PHONY: compounds
compounds: $(foreach dataset,$(DATASET_NAMES),$(DATA)/datasets/$(dataset)/compounds.json)
.PHONY: clusters
clusters: $(foreach dataset,$(DATASET_NAMES),$(DATA)/datasets/$(dataset)/clusters.gbk)
.PHONY: ani
ani: $(foreach dataset,$(DATASET_NAMES),$(DATA)/datasets/$(dataset)/ani.hdf5)
# --- External data ----------------------------------------------------------
$(PFAM_HMM):
$(WGET) http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam$(PFAM_VERSION)/Pfam-A.hmm.gz -O- | gunzip > $@
$(PGAP_HMM):
$(WGET) ftp://ftp.ncbi.nlm.nih.gov/hmm/11.0/hmm_PGAP.LIB -O $@
$(SMCOGS_HMM):
$(PYTHON) $(SCRIPTS)/smcogs/download.py --version $(SMCOGS_VERSION) --output $@
$(TAXONOMY)/taxdmp_$(TAXONOMY_VERSION).zip:
mkdir -p $(TAXONOMY)
$(WGET) https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_$(TAXONOMY_VERSION).zip -O $@
$(TAXONOMY)/%.dmp: $(TAXONOMY)/taxdmp_$(TAXONOMY_VERSION).zip
unzip $< -d $(TAXONOMY) $(notdir $@)
touch $@
# --- InterPro ---------------------------------------------------------------
$(GO_OBO):
$(WGET) http://purl.obolibrary.org/obo/go/releases/$(GO_VERSION)/go.obo -O $@
$(INTERPRO_XML):
$(WGET) https://ftp.ebi.ac.uk/pub/databases/interpro/releases/$(INTERPRO_VERSION)/interpro.xml.gz -O $@
$(INTERPRO_JSON): $(GO_OBO) $(INTERPRO_XML)
python $(SCRIPTS)/pfam/interpro_json.py --go $(GO_OBO) --xml $(INTERPRO_XML) --out $@
# --- NP Atlas ---------------------------------------------------------------
$(ATLAS):
$(WGET) https://www.npatlas.org/static/downloads/NPAtlas_download.json -O- | gzip -c > $@
$(DATA)/npatlas/classes.hdf5: $(CHEMONT) $(ATLAS)
$(PYTHON) $(SCRIPTS)/npatlas/make_classes.py --atlas $(ATLAS) --chemont $(CHEMONT) -o $@
$(DATA)/npatlas/maccs.hdf5: $(ATLAS)
$(PYTHON) $(SCRIPTS)/npatlas/make_maccs.py --atlas $(ATLAS) -o $@
# --- Generic Rules ----------------------------------------------------------
#$(DATA)/datasets/%/mibig3.1_ani.hdf5: $(DATA)/datasets/%/clusters.gbk $(DATA)/datasets/mibig3.1/clusters.gbk
# $(PYTHON) $(SCRIPTS)/common/make_ani.py --query $< --target $(DATA)/datasets/mibig3.1/clusters.gbk -o $@
$(DATA)/datasets/%/features.hdf5: $(DATA)/datasets/%/clusters.gbk $(PFAM_HMM)
$(PYTHON) -m chamois.cli annotate --i $< --hmm $(PFAM_HMM) -o $@
$(DATA)/datasets/%/classes.hdf5: $(DATA)/datasets/%/compounds.json $(ATLAS) $(CHEMONT)
$(PYTHON) $(SCRIPTS)/common/make_classes.py -i $< -o $@ --atlas $(ATLAS) --chemont $(CHEMONT) --cache $(BUILD) $(WISHART)
$(DATA)/datasets/%/maccs.hdf5: $(DATA)/datasets/%/compounds.json $(ATLAS) $(CHEMONT)
$(PYTHON) $(SCRIPTS)/common/make_maccs.py -i $< -o $@
$(DATA)/datasets/%/ani.hdf5: $(DATA)/datasets/%/clusters.gbk $(CHEMONT)
$(PYTHON) $(SCRIPTS)/common/make_ani.py -q $< -r $< -o $@ -s 0.3
$(DATA)/datasets/%/aci.mibig3.hdf5: $(DATA)/datasets/%/clusters.gbk $(DATA)/datasets/mibig3.1/clusters.gbk
$(PYTHON) $(SCRIPTS)/common/make_aci.py --query $(word 1,$^) --target $(word 2,$^) -o $@
# --- Download MIBiG 2.0 data ------------------------------------------------
$(DATA)/datasets/mibig2.0/clusters.gbk: $(DATA)/mibig/blocklist.tsv $(SCRIPTS)/mibig/download_records.py
$(PYTHON) $(SCRIPTS)/mibig/download_records.py --blocklist $< --mibig-version 2.0 -o $@
$(DATA)/datasets/mibig2.0/compounds.json: $(DATA)/mibig/blocklist.tsv $(ATLAS) $(SCRIPTS)/mibig/download_compounds.py
$(PYTHON) $(SCRIPTS)/mibig/download_compounds.py --blocklist $< --mibig-version 2.0 -o $@ --atlas $(ATLAS) --cache $(BUILD)
$(DATA)/datasets/mibig2.0/taxonomy.tsv: $(DATA)/mibig/blocklist.tsv $(TAXONOMY)/names.dmp $(TAXONOMY)/nodes.dmp $(TAXONOMY)/merged.dmp
$(PYTHON) $(SCRIPTS)/mibig/download_taxonomy.py --blocklist $< --mibig-version 2.0 -o $@ --taxonomy $(TAXONOMY)
# --- Download MIBiG 3.1 data ------------------------------------------------
$(DATA)/datasets/mibig3.1/clusters.gbk: $(DATA)/mibig/blocklist.tsv $(SCRIPTS)/mibig/download_records.py
$(PYTHON) $(SCRIPTS)/mibig/download_records.py --blocklist $< --mibig-version 3.1 -o $@
$(DATA)/datasets/mibig3.1/compounds.json: $(DATA)/mibig/blocklist.tsv $(ATLAS) $(SCRIPTS)/mibig/download_compounds.py
$(PYTHON) $(SCRIPTS)/mibig/download_compounds.py --blocklist $< --mibig-version 3.1 -o $@ --atlas $(ATLAS) --cache $(BUILD)
$(DATA)/datasets/mibig3.1/taxonomy.tsv: $(DATA)/mibig/blocklist.tsv $(TAXONOMY)/names.dmp $(TAXONOMY)/nodes.dmp $(TAXONOMY)/merged.dmp
$(PYTHON) $(SCRIPTS)/mibig/download_taxonomy.py --blocklist $< --mibig-version 3.1 -o $@ --taxonomy $(TAXONOMY)
# --- Download PRISM data ----------------------------------------------------
$(DATA)/prism4/BGCs.tar:
mkdir -p $(DATA)/datasets/prism4
$(WGET) https://zenodo.org/records/3985982/files/BGCs.tar?download=1 -O $@
$(DATA)/prism4/predictions.xlsx:
mkdir -p $(DATA)/datasets/prism4
$(WGET) https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-19986-1/MediaObjects/41467_2020_19986_MOESM5_ESM.xlsx -O $@
$(DATA)/datasets/prism4/clusters.gbk: $(DATA)/prism4/BGCs.tar $(DATA)/prism4/predictions.xlsx
$(PYTHON) $(SCRIPTS)/prism4/extract_records.py -i $< -o $@ --table $(word 2,$^)
$(DATA)/datasets/prism4/compounds.json: $(DATA)/prism4/predictions.xlsx $(ATLAS) $(DATA)/datasets/prism4/clusters.gbk
$(PYTHON) $(SCRIPTS)/prism4/extract_compounds.py -i $< -o $@ --atlas $(word 2,$^) --cache $(BUILD) --clusters $(word 3,$^)
# --- Download JGI data ------------------------------------------------------
$(BUILD)/abc/genomes.json:
mkdir -p $(BUILD)/abc
$(PYTHON) $(SCRIPTS)/abc/download_genomes.py -o $@
$(BUILD)/abc/clusters.json: $(BUILD)/abc/genomes.json
$(PYTHON) $(SCRIPTS)/abc/download_clusters.py -i $< -o $@
$(DATA)/datasets/abc/clusters.gbk: $(BUILD)/abc/clusters.json
$(PYTHON) $(SCRIPTS)/abc/download_records.py -i $< -o $@
$(DATA)/datasets/abc/compounds.json: $(BUILD)/abc/clusters.json $(ATLAS)
mkdir -p build/cache/abc_compounds
$(PYTHON) $(SCRIPTS)/abc/download_compounds.py --input $< --output $@ --atlas $(ATLAS) --cache $(BUILD)
# --- Download GenBank data ------------------------------------------------------
$(DATA)/datasets/nuccore/clusters.gbk: $(DATA)/datasets/nuccore/compounds.json
$(PYTHON) $(SCRIPTS)/nuccore/download_clusters.py --compounds $< --clusters $@
$(DATA)/datasets/nuccore-lite/clusters.gbk: $(DATA)/datasets/nuccore-lite/compounds.json $(DATA)/datasets/nuccore-lite/coordinates.tsv
$(PYTHON) $(SCRIPTS)/nuccore/download_clusters.py --compounds $< --clusters $@ --coordinates $(word 2,$^)
$(DATA)/datasets/native/clusters.gbk: $(DATA)/datasets/native/compounds.json $(DATA)/datasets/native/coordinates.tsv
$(PYTHON) $(SCRIPTS)/nuccore/download_clusters.py --compounds $< --clusters $@ --coordinates $(word 2,$^)