Merge v3b into master

.gitignore

@@ -1,2 +1,10 @@
 data/
 *.pyc
+*.o
+amr_report
+amrfinder
+fasta_check
+point_mut
+gff_check
+amrfinder_update
+fasta2parts

Makefile

@@ -1,47 +1,50 @@
+##############################################################################
+# PUBLIC DOMAIN NOTICE This software/database is "United States Government
+# Work" under the terms of the United States Copyright Act. It was written as
+# part of the authors' official duties for the United States Government and
+# thus cannot be copyrighted. This software/database is freely available to the
+# public for use without a copyright notice. Restrictions cannot be placed on
+# its present or future use.
+#
+# Although all reasonable efforts have been taken to ensure the accuracy and
+# reliability of the software and data, the National Center for Biotechnology
+# Information (NCBI) and the U.S. Government do not and cannot warrant the
+# performance or results that may be obtained by using this software or data.
+# NCBI, NLM, and the U.S. Government disclaim all warranties as to performance,
+# merchantability or fitness for any particular purpose.
+#
+# In any work or product derived from this material, proper attribution of the
+# authors as the source of the software or data should be made, using:
+# https://ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/ as the
+# citation.
+###############################################################################
+
 # the SVNREV is set automatically here for convenience,
 # but when actually building we should override it like:
 # make all SVNREV=-D\'SVN_REV=\"$VERSION\"\' or use
 # a version.txt file
 ifeq ($(wildcard version.txt),)
-	VERSION_STRING := $(shell svnversion -n .)
+	VERSION_STRING := $(shell git describe --tags)
 else
 	VERSION_STRING := $(shell cat version.txt)
 endif
 SVNREV := -D'SVN_REV="$(VERSION_STRING)"'
 
-SHELL=/bin/sh
-INSTALL = install
+# Define default paths
+PREFIX ?= /usr/local
+INSTALL=install
 
-CPPFLAGS = -std=gnu++11 \
-  -malign-double -fno-math-errno \
-  -Wall -Wextra \
-  -Wcast-align -Wconversion -Wdeprecated-declarations -Wformat -Winit-self -Wlogical-op \
-  -Wmissing-braces -Wmissing-field-initializers -Wmissing-format-attribute -Wmissing-include-dirs \
-  -Woverloaded-virtual -pedantic -Wparentheses -Wpointer-arith -Wsequence-point -Wshadow -Wunused \
-  -Wsuggest-attribute=format -Wswitch -Wuninitialized -Wsign-conversion -Wuseless-cast \
-  -O3 \
-  $(SVNREV) \
-  -Wno-error=misleading-indentation -Wno-nonnull-compare \
+CPPFLAGS = -std=gnu++11 -pthread -malign-double -fno-math-errno -O3 \
 
 CXX=g++
-COMPILE.cpp= $(CXX) $(CPPFLAGS)  -c
-
-#prefix = /panfs/pan1.be-md.ncbi.nlm.nih.gov/bacterial_pathogens/backup
-prefix=/usr/local
-
-# soft links are created here to INSTALL_DIR
-bindir="$(prefix)/bin"
+COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) -c 
 
-datadir=$(prefix)/share
 
-# This is where AMRFinder and the default database will be installed
-INSTALL_DIR=$(datadir)/amrfinder
+.PHONY: all clean install release
 
+BINARIES= amr_report amrfinder amrfinder_update fasta_check fasta2parts gff_check point_mut 
 
-.PHONY: all clean install dist
-DISTFILES = Makefile *.cpp *.hpp *.inc test_* amrfinder.pl AMRFinder-dna.sh AMRFinder-prot.sh fasta_check gff_check amr_report
-
-all:	amr_report fasta_check gff_check
+all:	$(BINARIES)
 
 release: clean
 	svnversion . > version.txt
@@ -55,35 +58,66 @@ amr_reportOBJS=amr_report.o common.o gff.o
 amr_report:	$(amr_reportOBJS)
 	$(CXX) -o $@ $(amr_reportOBJS)
 
-fasta_check.o:	common.hpp common.inc
-fasta_checkOBJS=fasta_check.o common.o
+amrfinder.o:  common.hpp common.inc amrfinder.inc
+amrfinderOBJS=amrfinder.o common.o
+amrfinder:	$(amrfinderOBJS)
+	$(CXX) -o $@ $(amrfinderOBJS) -pthread 
+
+amrfinder_update.o:  common.hpp common.inc amrfinder.inc
+amrfinder_updateOBJS=amrfinder_update.o common.o
+amrfinder_update:      $(amrfinder_updateOBJS)
+	$(CXX) -o $@ $(amrfinder_updateOBJS) -lcurl
+
+fasta_check.o:	common.hpp common.inc 
+fasta_checkOBJS=fasta_check.o common.o 
 fasta_check:	$(fasta_checkOBJS)
 	$(CXX) -o $@ $(fasta_checkOBJS)
 
+fasta2parts.o:	common.hpp common.inc
+fasta2partsOBJS=fasta2parts.o common.o
+fasta2parts:	$(fasta2partsOBJS)
+	$(CXX) -o $@ $(fasta2partsOBJS)
+
 gff_check.o:	common.hpp common.inc gff.hpp
 gff_checkOBJS=gff_check.o common.o gff.o
 gff_check:	$(gff_checkOBJS)
 	$(CXX) -o $@ $(gff_checkOBJS)
 
+point_mut.o:	common.hpp common.inc 
+point_mutOBJS=point_mut.o common.o
+point_mut:	$(point_mutOBJS)
+	$(CXX) -o $@ $(point_mutOBJS)
+
+
 clean:
 	rm -f *.o
-	rm -f amr_report fasta_check gff_check
-	#rm version.txt
+	rm -f $(BINARIES)
 
 install:
-	$(INSTALL) -D -t $(INSTALL_DIR) amr_report fasta_check gff_check amrfinder.pl
-#	@dest=$(INSTALL_DIR); \
-#		if [ ! -e $(bindir)/amrfinder.pl ]; \
-#		then \
-#			ln -s "$$dest/amrfinder.pl" $(bindir); \
-#			ln -s "$$dest/amr_report" $(bindir); \
-#			ln -s "$$dest/fasta_check" $(bindir); \
-#			ln -s "$$dest/gff_check" $(bindir); \
-#		else \
-#			echo "$$dest/amrfinder.pl already exists, so skipping link creation"; \
-#		fi
-
-DISTDIR=amrfinder.$(VERSION_STRING)
+	$(INSTALL) -D --target-directory=$(PREFIX)/bin $(BINARIES)
+
+# amrfinder binaries for github binary release
+GITHUB_FILE=amrfinder_binaries_v$(VERSION_STRING)
+GITHUB_FILES = test_* $(BINARIES)
+github_binaries:
+	@if [ ! -e version.txt ]; \
+	then \
+		echo >&2 "version.txt required to make a distribution file"; \
+		false; \
+	fi
+#   first recompile amrfinder.o to pick up the new version info
+	rm amrfinder.o amrfinder
+	make
+	mkdir $(GITHUB_FILE)
+	echo $(VERSION_STRING) > $(GITHUB_FILE)/version.txt
+	cp $(GITHUB_FILES) $(GITHUB_FILE)
+	if [ -e $(GITHUB_FILE).tar.gz ]; then rm $(GITHUB_FILE).tar.gz; fi
+	cd $(GITHUB_FILE); tar cvfz ../$(GITHUB_FILE).tar.gz *
+#	tar cvfz $(GITHUB_FILE).tar.gz $(GITHUB_FILE)/*
+	rm -r $(GITHUB_FILE)/*
+	rmdir $(GITHUB_FILE)
+
+DISTFILES=$(GITHUB_FILES) Makefile *.cpp *.hpp *.inc
 dist:
 	@if [ ! -e version.txt ]; \
 	then \
@@ -104,22 +138,20 @@ dist:
 	rm -r $(DISTDIR)/*
 	rmdir $(DISTDIR)
 
-# amrfinder binaries for github binary release
-GITHUB_FILE=amrfinder_binaries_v$(VERSION_STRING)
-GITHUB_FILES = test_* amrfinder.pl fasta_check gff_check amr_report
-github_binaries: all
-	@if [ ! -e version.txt ]; \
-	then \
-		echo >&2 "version.txt required to make a distribution file"; \
-		false; \
-	fi
-	mkdir $(GITHUB_FILE)
-	echo $(VERSION_STRING) > $(GITHUB_FILE)/version.txt
-	cp $(GITHUB_FILES) $(GITHUB_FILE)
-	sed "s/curr_version = .*/curr_version = '$(VERSION_STRING)';/" amrfinder.pl > $(GITHUB_FILE)/amrfinder.pl
-	if [ -e $(GITHUB_FILE).tar.gz ]; then rm $(GITHUB_FILE).tar.gz; fi
-	cd $(GITHUB_FILE); tar cvfz ../$(GITHUB_FILE).tar.gz *
-#	tar cvfz $(GITHUB_FILE).tar.gz $(GITHUB_FILE)/*
-	rm -r $(GITHUB_FILE)/*
-	rmdir $(GITHUB_FILE)
 
+test:
+	curl -O https://raw.githubusercontent.com/ncbi/amr/v3b/test_dna.fa \
+		-O https://raw.githubusercontent.com/ncbi/amr/v3b/test_prot.fa \
+		-O https://raw.githubusercontent.com/ncbi/amr/v3b/test_prot.gff \
+		-O https://raw.githubusercontent.com/ncbi/amr/v3b/test_both.expected \
+		-O https://raw.githubusercontent.com/ncbi/amr/v3b/test_dna.expected \
+		-O https://raw.githubusercontent.com/ncbi/amr/v3b/test_prot.expected
+	amrfinder --plus -p test_prot.fa -g test_prot.gff -O Campylobacter > test_prot.got
+	diff test_prot.expected test_prot.got
+	amrfinder --plus -n test_dna.fa -O Campylobacter > test_dna.got
+	diff test_dna.expected test_dna.got
+	amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Campylobacter > test_both.got
+	diff test_both.got test_both.expected
+
+
+     -O https://raw.githubusercontent.com/ncbi/amr/v3b/test_prot.expected

README.md

@@ -1,6 +1,6 @@
-# NCBI Antimicrobial Resistance Gene Finder (AMRFinder)
+# NCBI Antimicrobial Resistance Gene Finder (AMRFinderPlus)
 
-This software and the accompanying database are designed to find acquired antimicrobial resistance genes in protein or nucleotide sequences.
+This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences. We have also added "plus" stress, head, and biocide resistance as well as some virulence factors and E. coli antigens.
 
 ## See [the wiki for documentation](https://github.com/ncbi/amr/wiki)
 [Subscribe to our announce list](https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce) for announcements of  database or software updates.