First version including the rRNA detector

Former-commit-id: 865e2626c7cd92ea596aedefe2b760b3eaaa9c77
Former-commit-id: 94a2e642328eb679660c6ac5a6cb6803c2083632

detectors/rrna/tools/buildRRNAModels.sh

@@ -0,0 +1,165 @@
+#!/bin/bash
+#
+#                           BUILD RRNA models
+#
+#========================================================================================
+
+# -- 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"
+
+function fasta1li {
+
+    awk '/^>/ {if (sequence) \
+                  {print sequence}; \
+               print $0; \
+               sequence=""} \
+         !/^>/ {sequence = sequence $0} \
+         END {print sequence}' $1
+}
+
+function dereplicate {
+	DATA=$1
+	sumaclust -t 1 $DATA | \
+		fasta1li | \
+		grep -A 1 '^>' | \
+		grep -A1 'cluster_center=True;' | \
+		grep -v -- -- | \
+		sed -E "s/count=[0-9]+; //" | \
+		sed 's/cluster_weight/count/' | \
+		awk ' /^>/ {SEQ++;\
+		            match($0,"count=[0-9][0-9]*;");\
+		            count=substr($0,RSTART,RLENGTH);\
+		            $1=$1"_"SEQ;\
+		            print $1,count} \
+			 !/^>/ {print $0}'
+}
+
+
+function clustering {
+	DATA=$1
+	rm -rf $DATA
+	mkdir $DATA
+	sumaclust -t 0.9 $DATA.fasta | \
+		fasta1li > $DATA.clust.fasta
+	cluster=$(grep '^>' $DATA.clust.fasta | \
+	            sed -E 's/.*cluster=([^;]+);.*$/\1/' | \
+	            sort -u)
+	for c in $cluster; do
+		w=$(grep "$c" "${DATA}.clust.fasta" | \
+			head -1 | \
+			sed -E 's/.*cluster_weight=([^;]+);.*$/\1/')
+	    out=$(printf "${DATA}/%05d_%s" $w $c)
+        grep -A1  "$c" "${DATA}.clust.fasta" | \
+           grep -v -- -- > "$out.fasta"
+        muscle -in "$out.fasta" -out "$out.align.fasta"
+	done
+}
+
+function revcomp {
+    awk 'function printfasta(seq) {                                  \
+            seqlen=length(seq);                                       \
+            for (i=1; i <= seqlen; i+=60)                              \
+              print substr(seq,i,60);                                 \
+         }                                                          \
+        function comp(seq) {                                           \
+            "echo "seq" | tr acgtACGT tgcaTGCA " | getline res;     \
+            close("echo "seq" | tr acgtACGT tgcaTGCA "); \
+            return res;                                                \
+        }                                                              \
+        function rev(seq) {                                            \
+            "echo "seq" | rev " | getline res;                         \
+            close("echo "seq" | rev ");                                \
+            return res;                                                \
+        }                                                              \
+        function revcomp(seq) {                                        \
+            res=rev(comp(seq));                                        \
+            return res;                                                \
+        }                                                              \
+                                                                       \
+        (seq) && /^>/ {print head;                                     \
+                       printfasta(revcomp(seq));                       \
+                       seq=""}                                         \
+        /^>/   {head=$0}                                               \
+        ! /^>/ {seq=seq$0}                                             \
+        END { print head;                                     \
+              printfasta(revcomp(seq));                       \
+            }' $1
+}
+
+
+pushTmpDir ORG.buildRRNA
+
+	openLogFile "${RRNA_DATA_DIR}/rRNA_models.log"
+	
+	loginfo "Selecting Viridiplantae genebank entries..."
+		VIRIDIPLANTAE=$(${PROG_DIR}/../../normalize/tools/selectViridiplantae.sh $*) 
+		loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
+	loginfo "Done"
+	
+
+	loginfo "Extracting 4.5S rRNA sequences..."
+		${PROG_DIR}/extract_ref4.5S.sh ${VIRIDIPLANTAE} > raw_4_5S.fasta
+		loginfo " --> $(fastaCount raw_4_5S.fasta) retreived sequences"
+		dereplicate raw_4_5S.fasta > 4_5S.fasta
+		loginfo " --> $(fastaCount ${CALL_DIR}/4_5S.fasta) distinct sequences"
+	loginfo "Done"
+
+	loginfo "Clustering 4.5S rRNA sequences..."
+		clustering 4_5S
+	loginfo "Done"
+	
+	loginfo "Installing 4.5S rRNA sequences..."
+		cp -r 4_5S 	"${RRNA_DATA_DIR}/RRNA_4_5S"
+	loginfo "Done"
+	
+	loginfo "Extracting 5S rRNA sequences..."
+		${PROG_DIR}/extract_ref5S.sh ${VIRIDIPLANTAE} > raw_5S.fasta
+		loginfo " --> $(fastaCount raw_5S.fasta) retreived sequences"
+		dereplicate raw_5S.fasta > 5S.fasta
+		loginfo " --> $(fastaCount 5S.fasta) distinct sequences"
+	loginfo "Done"
+
+	loginfo "Clustering 5S rRNA sequences..."
+		clustering 5S
+	loginfo "Done"
+	
+	loginfo "Installing 5S rRNA sequences..."
+		cp -r 5S 	"${RRNA_DATA_DIR}/RRNA_5S"
+	loginfo "Done"
+	
+	
+	loginfo "Extracting 16S rRNA sequences..."
+		${PROG_DIR}/extract_ref16S.sh ${VIRIDIPLANTAE} > raw_16S.fasta
+		loginfo " --> $(fastaCount raw_16S.fasta) retreived sequences"
+		dereplicate raw_16S.fasta > 16S.fasta
+		loginfo " --> $(fastaCount 16S.fasta) distinct sequences"
+	loginfo "Done"
+
+	loginfo "Clustering 16S rRNA sequences..."
+		clustering 16S
+	loginfo "Done"
+	
+	loginfo "Installing 16S rRNA sequences..."
+		cp -r 16S 	"${RRNA_DATA_DIR}/RRNA_16S"
+	loginfo "Done"
+
+
+	loginfo "Extracting 23S rRNA sequences..."
+		${PROG_DIR}/extract_ref23S.sh ${VIRIDIPLANTAE} > raw_23S.fasta
+		loginfo " --> $(fastaCount raw_23S.fasta) retreived sequences"
+		dereplicate raw_23S.fasta > 23S.fasta
+		loginfo " --> $(fastaCount 23S.fasta) distinct sequences"
+	loginfo "Done"
+
+	loginfo "Clustering 23S rRNA sequences..."
+		clustering 23S
+	loginfo "Done"
+	
+	loginfo "Installing 23S rRNA sequences..."
+		cp -r 23S 	"${RRNA_DATA_DIR}/RRNA_23S"
+	loginfo "Done"
+
+
+popTmpDir