build rapidrun ref db

build_bdr_rapidrun.sh

+###############################################################################
+## RAPIDRUN
+SINGULARITY_SIMG="/media/superdisk/utils/conteneurs/obitools.simg"
+singularity shell --bind /media/superdisk:/media/superdisk $SINGULARITY_SIMG
+
+source ./config.sh
+
+for marker in `awk -F, '{ print $1}' infos/markers.csv`
+do
+	primer3=`grep $marker infos/markers.csv | cut -d, -f2`
+	primer5=`grep $marker infos/markers.csv | cut -d, -f3`
+	echo $marker $primer3 $primer5
+	MARKER_REF_DB_DIR="../"${marker}"_reference_database"
+	mkdir -p "${MARKER_REF_DB_DIR}"	
+	for DX in `ls "${rd_prefix}"*dx`
+	do
+		DX_PATH=`readlink -f $DX`
+		ln -s $DX_PATH $MARKER_REF_DB_DIR/$DX
+	done
+	cd "${MARKER_REF_DB_DIR}"
+	ecoPCR -d "${rd_prefix}" -e "${ecoPCR_e}" -l "${ecoPCR_l}" -L "${ecoPCR_L}" "${primer5}" "${primer3}" > v_"${rd_prefix}".ecopcr
+	obigrep -d "${rd_prefix}" --require-rank=species --require-rank=genus --require-rank=family v_"${rd_prefix}".ecopcr > v_"${rd_prefix}"_clean.fasta
+	obiuniq -d "${rd_prefix}" v_"${rd_prefix}"_clean.fasta > v_"${rd_prefix}"_clean_uniq.fasta
+	obigrep -d "${rd_prefix}" --require-rank=family v_"${rd_prefix}"_clean_uniq.fasta > v_"${rd_prefix}"_clean_uniq_clean.fasta
+	obiannotate --uniq-id v_"${rd_prefix}"_clean_uniq_clean.fasta > db_"${rd_prefix}".fasta
+	cd ../reference_database
+done