allows to change easiestly parameters

Former-commit-id: 8a6294012a853f94aba1443e4ac0056bdab3a0ac
Former-commit-id: f1f4fa2d1bc86494aab643090e6b06724b2923e3

detectors/normalize/lib/lookforIR.lib.sh

@@ -25,17 +25,18 @@ function lookForIR {
 		blastn -db ${SCDB} \
 		       -query ${QUERY} \
 		       -outfmt 6 \
-		       -max_target_seqs 10000 | \
+		       -max_target_seqs 10000  | \
-		  awk '($4 > 100) && ($3>80) { \
+		  awk -v id_match=80 -v lmin=100 \
-		             SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
+		     '($4 > lmin) && (($3+0)>id_match) { 
-			 		 if ($7 < $8) \
+		             SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); 
-			 			{print substr($2,1,3),$7,$8,SAME}  \
+			 		 if ($7 < $8) 
-			 		 else \
+			 			{print substr($2,1,3),$7,$8,SAME}  
-			 			{print substr($2,1,3),$8,$7,SAME}}' | \
+			 		 else 
+			 			{print substr($2,1,3),$8,$7,SAME}
+			  }' | \
 		  sort -nk 2 > ${MATCHES}
-	loginfo "Done"
+	loginfo "Done $(wc -l ${MATCHES} | awk '{print $1}') matches identified"
 
-	  
 	loginfo "Looking for long inverted repeats..."
 		repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
 		nrepeat="$(wc -l ${REPEATS} | awk '{print $1}')"

detectors/normalize/lib/selectIR.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys 
 from math import lgamma
@@ -32,6 +32,7 @@ for line in data:
         #    reverse complement = -1
         if direction==0:
             direction=-1
+
             
         if end > chlorosize:
             extsize =  end - chlorosize