Add scripts to generate reference DBs for LSC and SSC

Former-commit-id: 77fd69c9687bfc7cfd3305299c7c81d2a9eddada
Former-commit-id: 4d09933673c30d6a9b2b9cc985b33ef23d7a99f4

detectors/normalize/tools/buildSCDB.sh

@@ -0,0 +1,174 @@
+#!/bin/bash
+#
+#                           BUILD REFERENCE SINGLE COPY LIBRARIES
+#
+#========================================================================================
+
+# -- CAUTION -- Works as long than the script 
+#               is not called through a symlink
+SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
+source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
+
+pushTmpDir ORG.buildSCDB
+	
+	openLogFile "${IR_DATA_DIR}/SingleCopyDB.log"
+	
+	loginfo "Selecting Viridiplantae genebank entries..."
+		VIRIDIPLANTAE=$(${PROG_DIR}/selectViridiplantae.sh $*) 
+		loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
+	loginfo "Done"
+	
+	
+	#
+	# Deals with Long Single Copies (LSC)
+	#
+	
+	loginfo "Extracting Long Single Copies (LSC)..."
+		${PROG_DIR}/extract_refLSC.sh ${VIRIDIPLANTAE} > LSC.fasta
+		loginfo " --> $(fastaCount LSC.fasta) retreived sequences"
+	loginfo "Done"
+	
+	
+	
+	loginfo "Building LSC coorientation graph..."
+		${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${LOGFILE} > LSC.tgf
+		${PROG_DIR}/cc.py LSC.tgf > LSC.cc
+		loginfo " --> $(awk '{print $1}' LSC.cc | uniq | wc -l) connected componants"
+	loginfo "Done"
+
+
+	loginfo "Indexing LCS..."
+		fastaindex -f LSC.fasta -i LSC.index
+	loginfo "Done"
+	
+	
+	
+	loginfo "Extracting main connected components for LCS..."
+		rm -f LSC.direct.fasta
+		touch LSC.direct.fasta
+		for id in `awk '($1==0) {print $2}' LSC.cc`; do
+			fastafetch -f LSC.fasta -i LSC.index -q "${id}" >> LSC.direct.fasta
+		done
+		loginfo " --> $(fastaCount LSC.direct.fasta) sequences"
+	loginfo "Done"
+	
+	
+	
+	loginfo "Extracting second connected components for LCS..."
+		rm -f LSC.reverse.fasta
+		touch LSC.reverse.fasta
+		for id in `awk '($1==1) {print $2}' LSC.cc`; do
+			fastafetch -f LSC.fasta -i LSC.index -q "${id}" >> LSC.reverse.fasta
+		done		
+		loginfo " --> $(fastaCount LSC.reverse.fasta) sequences"
+	loginfo "Done"
+	
+	
+	
+	loginfo "merging both connected components for LCS..."
+		fastarevcomp LSC.reverse.fasta >> LSC.direct.fasta
+		loginfo " --> $(fastaCount LSC.direct.fasta) sequences in total"
+	loginfo "Done"
+
+
+
+	loginfo "Checking LCS homogeneity..."
+		${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${LOGFILE} > LSC_RefDB.tgf		
+		${PROG_DIR}/cc.py LSC_RefDB.tgf > LSC_RefDB.cc
+		NCC=$(awk '{print $1}' LSC_RefDB.cc | uniq | wc -l)
+		if (( $NCC == 1 )); then
+			loginfo " --> $NCC connected componants"
+		else
+			logwarning " --> $NCC connected componants"
+		fi
+	loginfo "Done"
+	
+	
+	
+	loginfo "Installing LCS reference databases..."
+		cp LSC.direct.fasta "${IR_DATA_DIR}/LSC_RefDB.fasta"
+		cp LSC_RefDB.tgf    "${IR_DATA_DIR}/LSC_RefDB.tgf"
+		
+		makeblastdb -in "${IR_DATA_DIR}/LSC_RefDB.fasta" \
+		            -dbtype nucl \
+		            -out "${IR_DATA_DIR}/LSC_RefDB" >& /dev/null
+	loginfo "Done"
+		
+	#
+	# Deals with Short Single Copies (SSC)
+	#
+	
+	loginfo "Extracting Short Single Copies (SSC)..."
+		${PROG_DIR}/extract_refSSC.sh ${VIRIDIPLANTAE} > SSC.fasta
+		loginfo " --> $(fastaCount SSC.fasta) retreived sequences"
+	loginfo "Done"
+
+
+	
+	loginfo "Building SSC coorientation graph..."
+		${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${LOGFILE} > SSC.tgf
+		${PROG_DIR}/cc.py SSC.tgf > SSC.cc
+		loginfo " --> $(awk '{print $1}' SSC.cc | uniq | wc -l) connected componants"
+	loginfo "Done"
+
+
+
+	loginfo "Indexing SSC..."
+		fastaindex -f SSC.fasta -i SSC.index
+	loginfo "Done"
+	
+	
+	
+	loginfo "Extracting main connected components for SSC..."
+		rm -f SSC.direct.fasta
+		touch SSC.direct.fasta
+		for id in `awk '($1==0) {print $2}' SSC.cc`; do
+			fastafetch -f SSC.fasta -i SSC.index -q "${id}" >> SSC.direct.fasta
+		done
+		loginfo " --> $(fastaCount SSC.direct.fasta) sequences"
+	loginfo "Done"
+	
+	
+	
+	loginfo "Extracting second connected components for SSC..."
+		rm -f SSC.reverse.fasta
+		touch SSC.reverse.fasta
+		for id in `awk '($1==1) {print $2}' SSC.cc`; do
+			fastafetch -f SSC.fasta -i SSC.index -q "${id}" >> SSC.reverse.fasta
+		done		
+		loginfo " --> $(fastaCount SSC.reverse.fasta) sequences"
+	loginfo "Done"
+	
+	
+	
+	loginfo "merging both connected components for SSC..."
+		fastarevcomp SSC.reverse.fasta >> SSC.direct.fasta
+		loginfo " --> $(fastaCount SSC.direct.fasta) sequences in total"
+	loginfo "Done"
+
+
+
+	loginfo "Checking SSC homogeneity..."
+		${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${LOGFILE} > SSC_RefDB.tgf		
+		${PROG_DIR}/cc.py SSC_RefDB.tgf > SSC_RefDB.cc
+		NCC=$(awk '{print $1}' SSC_RefDB.cc | uniq | wc -l)
+		if (( $NCC == 1 )); then
+			loginfo " --> $NCC connected componants"
+		else
+			logwarning " --> $NCC connected componants"
+		fi
+	loginfo "Done"
+	
+	
+	
+	loginfo "Installing SSC reference databases..."
+		cp SSC.direct.fasta "${IR_DATA_DIR}/SSC_RefDB.fasta"
+		cp SSC_RefDB.tgf    "${IR_DATA_DIR}/SSC_RefDB.tgf"
+		
+		makeblastdb -in "${IR_DATA_DIR}/SSC_RefDB.fasta" \
+		            -dbtype nucl \
+		            -out "${IR_DATA_DIR}/SSC_RefDB" >& /dev/null
+	loginfo "Done"
+		
+popTmpDir
+