First version of if inverted repeat annotation tools

Former-commit-id: 9d13deae459b086f11ba4f0f82aac899b4ff0fd9
Former-commit-id: 74a7f07d3fb26f6ce12808b8fe2dc7f176181285

detectors/normalize/lib/lookforIR.lib.sh

@@ -0,0 +1,53 @@
+source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
+
+SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
+
+function lookForIR {
+
+	local QUERY="$1"
+	local MATCHES=$(basename ${QUERY})
+	      MATCHES="${MATCHES/.*/}.matches"
+	
+	local REPEATS="${MATCHES/.*/}.repseek"
+	
+	loginfo "Locating SSC and LSC by similarity..."
+		blastn -db ${SCDB} \
+		       -query ${QUERY} \
+		       -outfmt 6 \
+		       -max_target_seqs 10000 | \
+		  awk '($4 > 1000) && ($3>80) { \
+		             SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
+			 		 if ($7 < $8) \
+			 			{print substr($2,1,3),$7,$8,SAME}  \
+			 		 else \
+			 			{print substr($2,1,3),$8,$7,SAME}}' | \
+		  sort -nk 2 > ${MATCHES}
+	loginfo "Done"
+	  
+	loginfo "Looking for long inverted repeats..."
+		repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
+		loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
+	loginfo "Done"
+	
+	loginfo "Marking and selecting the best inverted repeat..."
+		local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
+	loginfo "Done"
+	
+	loginfo " --> IR size : IRa = ${IR[5]} /  IRb = ${IR[7]}"
+	loginfo " --> IR Score: ${IR[8]}"
+	
+	let "deltaIR=${IR[5]} -  ${IR[7]}"
+	
+	if (( $deltaIR < -10 )) ||  (( $deltaIR > 10 )); then
+		logwarning "Differences between IR lengths ($deltaIR) is greater than 10"
+	fi
+	
+	
+	echo "${IR[@]}"
+}
+
+SCDB="${IR_DATA_DIR}/SC_RefDB"
+QUERY="${CALL_DIR}/$1"
+
+
+openLogFile "${QUERY/.*/}.log"

detectors/normalize/lib/selectIR.py

@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+
+import sys 
+
+data    = open(sys.argv[1])
+repeats = open(sys.argv[2])
+
+chloro    = {'LSC' : [], 'SSC' : [] }
+chlorosize =0
+
+for line in data:
+    parts = line.strip().split()
+    if len(parts) >= 4:
+        single      = parts[0]
+        begin       = int(parts[1])
+        end         = int(parts[2])
+        direction   = int(parts[3])
+        
+        
+        if direction==0:
+            direction=-1
+            
+        if end > chlorosize:
+            extsize =  end - chlorosize 
+            chloro['LSC'].extend([0] * extsize)
+            chloro['SSC'].extend([0] * extsize)
+            chlorosize=len(chloro['LSC'])
+        
+        begin-=1
+        
+        chr = chloro[single]
+        
+        for p in range(begin,end):
+            chr[p]+=direction
+   
+maxSSC = float(max(abs(n) for n in chloro['SSC']))
+maxLSC = float(max(abs(n) for n in chloro['LSC']))
+
+chloro['SSC']=[n / maxSSC for n in chloro['SSC']]
+chloro['LSC']=[n / maxLSC for n in chloro['LSC']]
+
+
+scoreMax=0
+imax = len(chloro['LSC'])
+
+for line in repeats:
+    parts   = line.strip().split()
+    
+    pos1    = int(parts[1]) -1
+    len1    = int(parts[3])
+    
+    pos2    = int(parts[2]) -1
+    len2    = int(parts[4])
+    
+    c_begin = min(pos1 + len1,imax)
+    c_end   = min(pos2,imax)
+    o_max   = min(pos1 ,imax)
+    o_min   = min(pos2 + len2, imax)
+    
+    c_lsc   = sum(abs(chloro['LSC'][n]) for n in range(c_begin,c_end))
+    c_ssc   = sum(abs(chloro['SSC'][n]) for n in range(c_begin,c_end))
+
+    o_lsc   = sum(abs(chloro['LSC'][n]) for n in range(0,o_max))
+    o_ssc   = sum(abs(chloro['SSC'][n]) for n in range(0,o_max))
+
+    o_lsc  += sum(abs(chloro['LSC'][n]) for n in range(o_min,len(chloro['LSC'])))
+    o_ssc  += sum(abs(chloro['SSC'][n]) for n in range(o_min,len(chloro['SSC'])))
+    
+    c = float(c_lsc + c_ssc)
+    o = float(o_lsc + o_ssc)
+    
+    if c > 0:
+        c_lsc /= c
+        c_ssc /= c 
+    
+    if o > 0:
+        o_lsc /= o 
+        o_ssc /= o 
+    
+    score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
+    
+    # print >>sys.stderr,"c.lsc = %f c.ssc = %f   o.lsc = %f o.ssc = %f score = %6.4f (len=%d)" % (c_lsc,c_ssc,o_lsc,o_ssc,score,len1)
+        
+    if (score > scoreMax):
+        scoreMax = score
+        pos1Max  = pos1
+        pos2Max  = pos2
+        len1Max  = len1
+        len2Max  = len2
+        
+c_begin = min(pos1Max + len1Max,imax)
+c_end   = min(pos2Max,imax)
+o_max   = min(pos1Max,imax)
+o_min   = min(pos2Max + len2Max,imax)
+
+c_lsc   = sum(chloro['LSC'][n] for n in range(c_begin,c_end))
+c_ssc   = sum(chloro['SSC'][n] for n in range(c_begin,c_end))
+
+o_lsc   = sum(chloro['LSC'][n] for n in range(0,o_max))
+o_ssc   = sum(chloro['SSC'][n] for n in range(0,o_max))
+
+o_lsc  += sum(chloro['LSC'][n] for n in range(o_min,len(chloro['LSC'])))
+o_ssc  += sum(chloro['SSC'][n] for n in range(o_min,len(chloro['SSC'])))
+
+if abs(c_lsc) > abs(c_ssc):
+    center = "LSC"  
+    dcenter= "+" if c_lsc > 0 else "-"
+else:
+    center = "SSC"
+    dcenter= "+" if c_ssc > 0 else "-"
+
+if abs(o_lsc) > abs(o_ssc):
+    out    = "LSC"  
+    dout   = "+" if o_lsc > 0 else "-"
+else:
+    out    = "SSC"
+    dout   = "+" if o_ssc > 0 else "-"
+    
+    
+    
+sys.stdout.write("%s %s %s %s %d %d %d %d %6.5f\n" % (center,
+                                                      dcenter,
+                                                      out,
+                                                      dout,
+                                                      pos1Max + 1,
+                                                      len1Max,
+                                                      pos2Max + 1,
+                                                      len2Max,
+                                                      scoreMax))
+    
+    
+         
+#for p in range(chlorosize):
+#    sys.stdout.write("%d %d %d\n"  % (p,chloro['SSC'][p],chloro['LSC'][p]))
+