request2dissim.sh has 4 parameters

phylogeny/distTree_inc_place_seq.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+THIS=`dirname $0`
+source $THIS/../bash_common.sh
+if [ $# -ne 2 ]; then
+  echo "Find the place of a sequence in a sequecne incremewntal tree"
+  echo "#1: sequence file"
+  echo "#2: incremental tree directory"
+  exit 1
+fi
+QUERY=$1
+INC=$2  
+
+
+TMP=`mktemp`  
+#echo $TMP  
+
+
+NAME=`basename $QUERY`
+$THIS/../genetics/dna_closest.sh $QUERY $INC/seq.fa | sed 's/$/ '$NAME'/1' > $TMP.request
+
+cp /dev/null $TMP.dissim
+echo "FAIL" > $TMP.leaf
+VARIANCE=`cat $INC/variance`
+while [ -s $TMP.request ]; do
+  $INC/request2dissim.sh $TMP.request $QUERY $TMP.dissim-add $TMP.log &> /dev/null
+  rm $TMP.request
+  cat $TMP.dissim-add >> $TMP.dissim
+  $THIS/../phylogeny/distTree_new  $INC/  -variance $VARIANCE  -name $NAME  -dissim $TMP.dissim  -request $TMP.request  -leaf $TMP.leaf
+done
+
+L=(`cat $TMP.leaf`)
+echo "${L[0]} has arc of length ${L[2]} joining above ${L[1]} by ${L[3]}"
+
+
+rm -fr $TMP*
+

phylogeny/distTree_inc_request.sh

@@ -19,7 +19,7 @@ DIR=$1/search/$2
 LOG=$1/log/$2
 
 
-$1/request2dissim.sh $DIR/request $DIR/dissim.add $LOG &> $LOG.request2dissim
+$1/request2dissim.sh $DIR/request "" $DIR/dissim.add $LOG &> $LOG.request2dissim
 if [ ! -s $DIR/dissim.add ]; then
   echo "Empty $DIR/dissim.add" > $LOG
   exit 1

phylogeny/distTree_inc_request2dissim.sh

@@ -36,7 +36,7 @@ else
 		ls $INC/dr > $INC/dr.list
 		while [ -s $INC/dr.list ]; do
 		  $THIS/../grid_wait.sh 1
-  		$THIS/../trav  -step 1  $INC/dr.list "$QSUB_5 -N j%f %q$INC/request2dissim.sh $INC/dr/%f $INC/dr.out/%f $INC/dr.out/%f.log%q > /dev/null"		
+  		$THIS/../trav  -step 1  $INC/dr.list "$QSUB_5 -N j%f %q$INC/request2dissim.sh $INC/dr/%f %Q%Q $INC/dr.out/%f $INC/dr.out/%f.log%q > /dev/null"		
   		$THIS/../qstat_wait.sh 2000 1	
  			set +o errexit	
 		  ls $INC/dr.out | grep    '\.log$' | sed 's/\.log$//1' > $INC/dr.bad

version.inc

@@ -1,6 +1,7 @@
-#define VERSION "1.1.11"
+#define VERSION "1.2.1"
 
 
+// 1.2.1  08/20/2020  request2dissim.sh: 4 parameters
 // 1.1.12 07/28/2020  Newick import removes transient nodes; printDistTree: 'itree' --> 'dm'
 // 1.1.11 07/27/2020  improvement of Func::findZero(); statDistTree: length precision is increased; DistTree::saveFeatureTree(withTime); Feature::getLambda()
 // 1.1.10 07/18/2020  makeDistTree -min_arc_prob; DistTree::reroot() does not use 3*SD