103 lines
3.3 KiB
Makefile
103 lines
3.3 KiB
Makefile
SHELL := /bin/bash
|
|
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
|
GBURL=https://$(FTPNCBI)/genbank
|
|
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
|
|
|
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
|
|
|
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
|
|
|
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
|
| grep -E 'gb.+\.seq\.gz' \
|
|
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
|
| sort \
|
|
| uniq)
|
|
|
|
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
|
DIRECTORIES=fasta fasta_fgs
|
|
|
|
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
|
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
|
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
|
|
|
|
|
SUFFIXES += .d
|
|
NODEPS:=clean taxonomy
|
|
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
|
|
|
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
|
#Chances are, these files don't exist. GMake will create them and
|
|
#clean up automatically afterwards
|
|
-include $(DEPFILES)
|
|
endif
|
|
|
|
|
|
all: depends directories FORCE
|
|
@make downloads
|
|
|
|
downloads: taxonomy fasta_files
|
|
@echo Genbank Release number $(GBRELEASE)
|
|
@echo all divisions : $(GBDIV_ALL)
|
|
|
|
FORCE:
|
|
|
|
.PHONY: all directories depends taxonomy fasta_files FORCE
|
|
|
|
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
|
|
|
division: $(GBDIV)
|
|
|
|
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
|
|
|
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
|
|
|
Release_$(GBRELEASE):
|
|
@mkdir -p $@
|
|
@echo Create $@ directory
|
|
|
|
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
|
@mkdir -p $@
|
|
@echo Create $@ directory
|
|
|
|
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
|
@mkdir -p $@
|
|
@echo Create $@ directory
|
|
|
|
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
|
@mkdir -p $@
|
|
@echo Create $@ directory
|
|
|
|
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
|
@echo Create depends directory
|
|
@mkdir -p Release_$(GBRELEASE)/depends
|
|
@for f in ${GBFILE_ALL} ; do \
|
|
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
|
echo -e "\t@echo Downloading file : $$f..." ; \
|
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
|
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
|
echo ; \
|
|
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
|
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
|
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
|
fasta_files="$$fasta_files $$fasta" ; \
|
|
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
|
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
|
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
|
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
|
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
|
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
|
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
|
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
|
echo -e "\t || rm -f \$$@" ; \
|
|
echo -e "\t@echo conversion of $$@ done." ; \
|
|
echo ; \
|
|
done > $@ ; \
|
|
echo >> $@ ; \
|
|
echo "fasta_files: $$fasta_files" >> $@ ;
|
|
|
|
Release_$(GBRELEASE)/taxonomy:
|
|
mkdir -p $@
|
|
curl -iL $(TAXOURL) \
|
|
| tar -C $@ -zxf -
|