Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate

Former-commit-id: 14936719198c993d2e38b2c4d8f78dfa5c46c0b4
Former-commit-id: 8e795225e073e077fbc6835b9d9746b6c6ed95cf

config/default.conf

@@ -118,9 +118,9 @@ INCDIR	 =	$(abspath $(PRTDIR))/include
 # default gmake variable in implicit rules
 # ------------------------------------
 
-CFLAGS 	  = 	$(OPTIM) $(MACHDEF) -I$(INCDIR)
+CFLAGS 	  := $(CFLAGS)	$(OPTIM) $(MACHDEF) -I$(INCDIR)
 
-LDFLAGS	  =     -L$(LIBDIR) -L.
+LDFLAGS	  := $(LDFLAGS)    -L$(LIBDIR) -L.
 
 LDLIBS	  =	    $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
 

detectors/normalize/bin/go_normalize.sh

@@ -100,7 +100,7 @@ pushTmpDir ORG.normalize
 	tmpLSC="tmp_$$_LSC.fasta"		
 	tmpSSC="tmp_$$_SSC.fasta"		
 	
-	# Extract the first SC present in between the two IRs
+	# Extract the central SC present in between the two IRs
 	# considering it as LSC
 
 	let "beginLSC=$endIR1+1"
@@ -110,7 +110,7 @@ pushTmpDir ORG.normalize
 	strandLSC="${IR[1]}"
 
 
-	# Extract the second SC present in two parts
+	# Extract the external SC present in two parts
 	# Considering it as SSC
 	
 	let "beginSSC=$endIR2+1"
@@ -130,16 +130,17 @@ pushTmpDir ORG.normalize
 	
 		# Actually this is the oposite LSC is SSC and SSC is LSC
 
-		# Exchange the SSC and LSC sequences
+		# Exchanges the SSC and LSC sequences
 		mv ${tmpSSC}    ${tmpfasta1}
 		mv ${tmpLSC}    ${tmpSSC}
 		mv ${tmpfasta1} ${tmpLSC}
 		
-		# Exchange the IRa and IRb sequences
+		# Exchanges the IRa and IRb sequences
 		mv ${tmpIR1}    ${tmpfasta1}
 		mv ${tmpIR2}    ${tmpIR1}
 		mv ${tmpfasta1} ${tmpIR2}
 		
+		# Exchanges the strand of both the Single copies
 		tmp=${strandSSC}
 		strandSSC=${strandLSC}
 		strandLSC=${tmp}
@@ -162,7 +163,6 @@ pushTmpDir ORG.normalize
 	cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
 
 	
-	
 popTmpDir
 
 exit 0

detectors/normalize/lib/lookforIR.lib.sh

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
@@ -10,12 +12,21 @@ function lookForIR {
 	
 	local REPEATS="${MATCHES/.*/}.repseek"
 	
+	# Blast columns:
+	# 	query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
+	# We keep blast matches if : 
+	#	The match is longer than 1000
+	#   The identity is higher than 80%
+	#
+	# The match file has the following format:
+	#	LSC/SSC  begin end  same_strand=1/diff_strand=0
+	
 	loginfo "Locating SSC and LSC by similarity..."
 		blastn -db ${SCDB} \
 		       -query ${QUERY} \
 		       -outfmt 6 \
 		       -max_target_seqs 10000 | \
-		  awk '($4 > 1000) && ($3>80) { \
+		  awk '($4 > 100) && ($3>80) { \
 		             SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
 			 		 if ($7 < $8) \
 			 			{print substr($2,1,3),$7,$8,SAME}  \
@@ -24,6 +35,7 @@ function lookForIR {
 		  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"

detectors/normalize/lib/selectIR.py

@@ -8,6 +8,12 @@ repeats = open(sys.argv[2])
 chloro    = {'LSC' : [], 'SSC' : [] }
 chlorosize =0
 
+# We scan the blast matches:
+#    We build a vector with one position per base pair counting the matches
+
+# The match file has the following format:
+#    LSC/SSC  begin end  same_strand=1/diff_strand=0
+
 for line in data:
     parts = line.strip().split()
     if len(parts) >= 4:
@@ -16,7 +22,8 @@ for line in data:
         end         = int(parts[2])
         direction   = int(parts[3])
         
-        
+        # Change the code of the direction:
+        #    reverse complement = -1
         if direction==0:
             direction=-1
             
@@ -39,32 +46,49 @@ 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
+len1Max=0
+len2Max=0
+
 imax = len(chloro['LSC'])
 
 for line in repeats:
     parts   = line.strip().split()
     
+    # First repeat position and length 
+    # (position start at 0)
     pos1    = int(parts[1]) -1
     len1    = int(parts[3])
     
+    # Second repeat position and length
+    # (position start at 0)
     pos2    = int(parts[2]) -1
     len2    = int(parts[4])
     
+    # Location of the central single copy 
+    #       - in between the two IR -
     c_begin = min(pos1 + len1,imax)
     c_end   = min(pos2,imax)
+    
+    # Location of the external single copy 
+    #       - in between the two IR -
     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))
+    # count of coherent matches for LSC and SSC on the central single copy 
-    c_ssc   = sum(abs(chloro['SSC'][n]) for n in range(c_begin,c_end))
+    c_lsc   = abs(sum(chloro['LSC'][n] for n in range(c_begin,c_end)))
+    c_ssc   = abs(sum(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))
+    # count of coherent matches for LSC and SSC on the external single copy 
-    o_ssc   = sum(abs(chloro['SSC'][n]) for n in range(0,o_max))
+    #    this score is in two parts before the first copy and after the second
+    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(abs(chloro['LSC'][n]) for n in range(o_min,len(chloro['LSC'])))
+    o_lsc  += sum(chloro['LSC'][n] for n in range(o_min,imax))
-    o_ssc  += sum(abs(chloro['SSC'][n]) for n in range(o_min,len(chloro['SSC'])))
+    o_ssc  += sum(chloro['SSC'][n] for n in range(o_min,imax))
+    
+    o_lsc   = abs(o_lsc)
+    o_ssc   = abs(o_ssc)
     
     c = float(c_lsc + c_ssc)
     o = float(o_lsc + o_ssc)
@@ -78,10 +102,9 @@ for line in repeats:
         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):
+    if (score >= scoreMax) and ((len1 > len1Max) or (len2 > len2Max)):
         scoreMax = score
         pos1Max  = pos1
         pos2Max  = pos2
@@ -99,8 +122,8 @@ 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_lsc  += sum(chloro['LSC'][n] for n in range(o_min,imax))
-o_ssc  += sum(chloro['SSC'][n] for n in range(o_min,len(chloro['SSC'])))
+o_ssc  += sum(chloro['SSC'][n] for n in range(o_min,imax))
 
 if abs(c_lsc) > abs(c_ssc):
     center = "LSC"  

detectors/trna/bin/go_trna.sh

@@ -33,7 +33,7 @@ pushTmpDir ORG.trna
 	TRNA=$(basename ${QUERY})
 	
 	aragorn -i -w -seq ${QUERY} | \
-		${PROG_DIR}/../lib/aragorn_wrapper.awk
+		${AwkCmd} -f ${PROG_DIR}/../lib/aragorn_wrapper.awk
 	
 
 popTmpDir

org-annotate.sh

@@ -34,19 +34,19 @@ pushTmpDir ORG.organnot
 	loginfo "Done."
 	
 	loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
-		${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"		
+		${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"		
 	loginfo "Done."
 	
 	loginfo "Annotating the tRNA..."
-		${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
+		${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
 	loginfo "Done."
 	
 	loginfo "Annotating the rRNA genes..."
-		${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
+		${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
 	loginfo "Done."
 
 	loginfo "Annotating the CDS..."
-		${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
+		${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
 	loginfo "Done."
 	
 	loginfo "Printing annotations header..."
@@ -96,11 +96,11 @@ pushTmpDir ORG.organnot
 			 		      freq["G"]" G; "\
 			 		      freq["T"]" T; "\
 			 		      other" other;" \
-			 }' ${QUERY}
+			 }' "${RESULTS}.norm.fasta"
 	loginfo "Done."
 	
 	loginfo "Reformating sequences..."
-		lines=$(wc -l ${QUERY} | awk '{print $1}')
+		lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
 		awk -v lines=$lines ' \
 			! /^>/ { \
 					seq=tolower($0); \
@@ -115,7 +115,7 @@ pushTmpDir ORG.organnot
 					if (NR==lines) \
 					  {pos-=1}; \
 					printf("   %6d\n",pos) \
-			   }' ${QUERY}
+			   }' "${RESULTS}.norm.fasta"
 	loginfo "Done."
 	
 	loginfo "Closing sequence part..."

scripts/bash_init.sh

@@ -19,7 +19,7 @@ function getAbsolutePath {
 # Manage temp directory
 
 function pushTmpDir {
-	TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
+	TMP_DIR=$(mktemp -d -t "$1_proc_$$_XXXXXX")
 	pushd $TMP_DIR >& /dev/null
 	TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
 	logdebug "Pushing temp directory $TMP_DIR"