From f39e66d4c1ea1af93cb4af4f86b999938f0ca1b9 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 18 Dec 2015 22:05:51 +0100
Subject: [PATCH] integrate options in the main script

Former-commit-id: e046ef88288559ed68463d3e9fd334ff0a8d1ec6
Former-commit-id: a2f99a532f7ce1b3114385c49affc197419a04d9
---
 config/targets/package.targ | 18 ++++++++---
 org-annotate.sh             | 62 ++++++++++++++++++++++++++++++++-----
 2 files changed, 67 insertions(+), 13 deletions(-)

diff --git a/config/targets/package.targ b/config/targets/package.targ
index 55733de..b4dd500 100644
--- a/config/targets/package.targ
+++ b/config/targets/package.targ
@@ -41,20 +41,28 @@ pkg.make:: pkg.expand
 	                               export LDFLAGS="$(LDFLAGS)" && \
 	                               cd $(PKGDIR) && \
 	                               ./configure --prefix=$(PRTPATH) $(CONFIGURE_OPTIONS)) 
-	$(MAKE) -C $(PKGDIR)
+	(export PATH="$(PRTPATH_BIN):$$PATH" && \
+	 export PKG_CONFIG=$(PKG_CONFIG) && \
+	 export CC="$(CC)" && \
+	 export CXX="$(CXX)" && \
+	 export CPP="$(CPP)" && \
+	 export CXXPP="$(CXXPP)" && \
+	 export CFLAGS="$(CFLAGS)" && \
+	 export LDFLAGS="$(LDFLAGS)" && \
+	 $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR))
 
 pkg.install:: pkg.make
-	$(MAKE) -C $(PKGDIR) install
+	$(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) install
 
 pkg:: pkg.install
 	@echo "+++++++++++ package $(PKG) done"
 
 test::
-	(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) test
+	(! test -d $(PKGDIR)) || $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) test
 
 clean::
-	(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) clean
+	(! test -d $(PKGDIR)) || $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) clean
 
 portclean::
-	(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) distclean
+	(! test -d $(PKGDIR)) || $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) distclean
 	(! test -d $(PKGDIR)) || \rm -r $(PKGDIR)
diff --git a/org-annotate.sh b/org-annotate.sh
index 993428f..f7cb9a6 100755
--- a/org-annotate.sh
+++ b/org-annotate.sh
@@ -14,6 +14,48 @@
 THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
 source "${THIS_DIR}/scripts/bash_init.sh"
 
+#
+# Management of options
+#
+
+taxid="no"
+normalization="yes"
+irdetection="yes"
+
+# options may be followed by one colon to indicate they have a required argument
+if ! options=$(getopt -o t:ih -l ncbi-taxid:,no-ir-detection,help -- "$@")
+then
+    # something went wrong, getopt will put out an error message for us
+    exit 1
+fi
+
+set -- $options
+
+while [ $# -gt 0 ]
+do
+    case $1 in
+    -t|--ncbi-taxid) taxid="$2" ; shift;;
+    -i|--no-ir-detection)  irdetection="no" ;;
+    -h|--help)  echo "Usage:" ;  
+    			echo "    $0 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \' 
+    			echo "       [-i|--no-ir-detection] [-h|--help] <FASTAFILE>"
+    			echo
+    			echo "Options:"
+    			echo '  -t ### | --ncbi-taxid ###'
+    			echo '      ### represents the ncbi taxid associated to the sequence'
+    			echo
+    			echo '  -i     | --no-ir-detection'
+    			echo '      Does not look for inverted repeats in the plastid genome'
+               	exit 0;;
+    (--) shift; break;;
+    (-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
+    (*) break;;
+    esac
+    shift
+done
+
+#############################
+
 pushTmpDir ORG.organnot
 
 	if [[ ! "$1" =~ ^/ ]]; then
@@ -27,15 +69,19 @@ pushTmpDir ORG.organnot
 	
 	rm -f ${LOG}
 	openLogFile ${LOG}
-
-	loginfo "Normalizing the structure of the Chloroplast sequence..."
-		loginfo "   LSC + IRB + SSC + IRA"
-		${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
-	loginfo "Done."
 	
-	loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
-		${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"		
-	loginfo "Done."
+	if [ "$irdetection"=="yes" ]; then
+
+		loginfo "Normalizing the structure of the Chloroplast sequence..."
+			loginfo "   LSC + IRB + SSC + IRA"
+			${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
+		loginfo "Done."
+		
+		loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
+			${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"		
+		loginfo "Done."
+		
+	fi
 	
 	loginfo "Annotating the tRNA..."
 		${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"