A new set of protein cleaned for the CDS detector prepared using the

clusterizecore.sh script from the detectors/cds/lib folder.

The CDS detector is now modified to use the clean.fst files.

detectors/cds/bin/do_exonerate.sh → detectors/cds/bin/do_exonerate.csh

@@ -31,7 +31,7 @@ set GenoName = `basename $GenoFile:r`
 
 set ProtFile = $Argv[1]; Shift
 set ProtDir  = `dirname $ProtFile`
-set ProtName = `basename $ProtFile:r`
+set ProtName = `basename $ProtFile | $AwkCmd -F'.' '{print $1}'`
 set ProtType = `basename $ProtDir`
 
 NeedFile $GenoFile
@@ -122,7 +122,7 @@ endif
 
 if ($PASS1_SPEEDUP != 0) then
 
-  tcsh -f $PROG_DIR/do_filterbx.sh $GenoFile $ProtFile  \
+  tcsh -f $PROG_DIR/do_filterbx.csh $GenoFile $ProtFile  \
             $PASS1_BLASTX_FILTER_IDMIN          \
             $PASS1_BLASTX_FILTER_NBMIN          \
             $PASS1_BLASTX_FILTER_NBMAX > D_$$

detectors/cds/bin/go_cds.sh → detectors/cds/bin/go_cds.csh

@@ -55,10 +55,10 @@ endif
 
 foreach dir ("core" "shell" "dust")
   if (-d $DbRoot/$dir) then
-    set fams = `ls $DbRoot/$dir/*.fst`
+    set fams = `ls $DbRoot/$dir/*.clean.fst`
     Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
     foreach f ($fams)
-      tcsh -f $PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
+      tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
     end
   endif
 end

detectors/cds/lib/bestclust.awk

@@ -3,6 +3,8 @@
 #
 # -v MAX_SPAN ALLOW_STOP EXCLUDE
 #
+# 
+#
 
 BEGIN {
   PROCINFO["sorted_in"] = "@ind_num_asc"

detectors/cds/lib/clustertizecore.sh

@@ -6,6 +6,9 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 CORELIB="${CDS_DATA_DIR}/chlorodb/core"
 
+CDHIT_ID=0.7
+CDHIT_DELTA=0.8
+
 
 function clusterize() {
  
@@ -17,12 +20,15 @@ function clusterize() {
  	rm -rf "${prot}"
  	mkdir -p "${prot}"
  	
- 	cd-hit -i "${fastain}" \
- 	       -o "${prot}/${cdhitout}" \
- 	       -c 0.6 -G 1 \
- 	       -g 1 -s 0.8 \
- 	       -b 150 -p 1 \
- 	       -d 0 -n 3
+ 	cd-hit 	-i "${fastain}" \
+ 	    	-o "${prot}/${cdhitout}" \
+ 	    	-c ${CDHIT_DELTA} \
+ 	    	-G 1 \
+			-g 1 \
+			-aL 0.95 \
+			-s ${CDHIT_ID} \
+ 	    	-b 350 -p 1 \
+ 	    	-d 0 -n 3
  	       
  	fasta1line "${fastain}" > "${prot}/${fasta1}"
  	
@@ -35,6 +41,8 @@ function clusterize() {
  	                 filename=prot".cluster."cluster".ids"; \
  	                 print $3 >> filename ; \
  	                 close(filename) }' "${cdhitout}.clstr"
+ 	                
+ 	rm -f "../$prot.clean.fst"
  	                 
  	for ids in *.cluster.*.ids ; do
  		cluster=$(printf "%03d" $(echo "${ids}" | $AwkCmd -F'.' '{print $3}'))
@@ -52,10 +60,10 @@ function clusterize() {
 	 	    egrep -v -- '^--$' > "$alignment"
 	    fi
 	 		
- 	    if (( size >= 10 )) ; then
+ 	    if (( size >= 5 )) ; then
  	    	egrep -f "$ids" -A 1 "${fasta1}" | \
 	 	    egrep -v -- '^--$' | \
-	 	    formatfasta >> "$prot.clean.fst"
+	 	    formatfasta >> "../$prot.clean.fst"
  	    fi
  	    
  	    rm -f "$ids"
@@ -73,6 +81,8 @@ function clusterize() {
 
 pushd $CORELIB
 
+rm -rf *.clean.fst
+
 for prot in *.fst ; do
 	prot="${prot/.fst/}"
 	clusterize "$prot"

detectors/normalize/lib/selectIR.py

 #!/usr/bin/env python
 
 import sys 
+from math import lgamma
+from math import log
 
 data    = open(sys.argv[1])
 repeats = open(sys.argv[2])
@@ -8,6 +10,10 @@ repeats = open(sys.argv[2])
 chloro    = {'LSC' : [], 'SSC' : [] }
 chlorosize =0
 
+def lpbinom(x,n,p):
+    lprob = log(p) * x + log(1-p) * (n-x) + lgamma(n+1) - lgamma(x+1) - lgamma(n-x+1)
+    return lprob
+
 # We scan the blast matches:
 #    We build a vector with one position per base pair counting the matches
 
@@ -102,6 +108,7 @@ for line in repeats:
         o_ssc /= o 
     
     score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
+    # pvalue= 
     # 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) and ((len1 > len1Max) or (len2 > len2Max)):

org-annotate.sh

@@ -151,7 +151,7 @@ pushTmpDir ORG.organnot
 					loginfo "Done."
 				
 					loginfo "Annotating the CDS..."
-						tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
+						tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.csh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
 					loginfo "Done."
 					
 					if (( partial == 0 )) ; then 

scripts/bash_init.sh

@@ -129,11 +129,13 @@ function fasta1line {
 }
 
 function formatfasta {
-	$AwkCmd  'function printfasta(seq) {                                \
+	$AwkCmd  'function printfasta(seq) {                            \
 									seqlen=length(seq);             \
 									for (i=1; i <= seqlen; i+=60)   \
 									   print substr(seq,i,60);      \
 								   }                                \
+								(seq && /^>/) { printfasta(seq);    \
+                                                seq=""}             \
 								/^>/   { print $0 }                 \
 								! /^>/ { seq=seq $0 }               \
 								END    { printfasta(seq)}' "${1}"