Add scripts to generate reference DBs for LSC and SSC

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

detectors/normalize/tools/coorienteSC.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+#
+#                           BUILD THE COORIENTATION GRAPH
+#
+# From a set of sequences, this commande build a graph where:
+#             - vertices are sequence id
+#             - relation is : s oriented in the same way
+#
+# The same ortientation is defined from the similiarity measured by blast
+# The result graph is formated following the tgf format (trivial graph format)
+#                 NODE1 NODE2 EDGE_LABEL
+#
+# Run the command
+#
+#   coorienteSC.sh <FASTA_FILE> <MINLENGTH> [LOGFILE]
+#
+#   <FASTA_FILE> : the fasta file containing sequences to analyse
+#   <MINLENGTH>  : the cumulative minimum length strand have to share to conclude
+#   <LOGFILE>    : an optional logfile name
+#
+#========================================================================================
+
+
+# -- 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.coorienteSC
+
+	if [[ ! -z $3 ]]; then
+		openLogFile $3
+	fi
+
+	DATA="${CALL_DIR}/${1}"
+	MINLENGTH=$2
+	BLASTDB=${1/.fasta$/}
+
+	loginfo "Build temporary blast DB..."
+	makeblastdb -in "${DATA}" -dbtype nucl -out "${BLASTDB}" >& /dev/null
+	loginfo "Done"
+	
+	loginfo "Running Blast..."
+		blastn -db "${BLASTDB}" -query "${DATA}" -outfmt 6 | \
+	 	awk ' \
+	 	      ($4 > 1000) && ($3 > 70) \
+	 	      ($1==QUERY) && \
+	 	      ($2==SUBJECT) && \
+	 	      (($7<$8) && ($9<$10)) || (($7>$8) && ($9>$10)) {LSAME+= ($3/100.*$4)} \
+	 	      ($4 > 1000) &&  ($3 > 70) \
+	 	      ($1==QUERY) && \
+	 	      ($2==SUBJECT) && \
+	 	      (($7<$8) && ($9>$10)) || (($7>$8) && ($9<$10)) {LDIFF+= ($3/100.*$4)} \
+	 	      (QUERY!="") && \
+	 	      (($1!=QUERY) || ($2!=SUBJECT)) {print QUERY,SUBJECT,LSAME,LDIFF,(LSAME>LDIFF)} \
+	 	      (($1!=QUERY) || ($2!=SUBJECT)) {QUERY=$1;SUBJECT=$2; \
+	 	                                      LSAME=0; \
+	 	                                      LDIFF=0; \
+	 	                                      if (($4 > 1000) && ($3 > 70)) { \
+	 	                                        if ((($7<$8) && ($9<$10)) || \
+	 	                                            (($7>$8) && ($9>$10))) {\
+	 	                                         LSAME= ($3/100.*$4) } \
+	 	                                      else { \
+	 	                                         LDIFF= ($3/100.*$4) }} \
+	 	                                     } \
+	          END {print QUERY,SUBJECT,LSAME,LDIFF,(LSAME>LDIFF)}' | \
+     	awk -v minlength="${MINLENGTH}" \
+     		  ' (($3>minlength) || \
+       			($4 > minlength)) && \
+       			($3/($4+1) > 2) && \
+       			($1!=$2) { if ($1 > $2) \
+       						 { print $2,$1,$5 } \
+                           else \
+                             {print $1,$2,$5}}' | \
+        sort | \
+        uniq -c | \
+        awk '($1==2) {print $2,$3,$4}'
+	loginfo "Done"
+	          
+popTmpDir
+
+