inc/{large,request_closest_sql} have 0 length

ncbi · Jan 25, 2021 · 79586a7 · 79586a7
1 parent 9acff85
commit 79586a7
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Showing 12 changed files with 40 additions and 21 deletions.
diff --git a/phylogeny/distTree_inc.sh b/phylogeny/distTree_inc.sh
@@ -116,7 +116,11 @@ $THIS/distTree_inc_tree1_quality.sh $INC
 
 if [ -e $INC/phen ]; then
 	DATE=`date +%Y%m%d`
-	LARGE=`cat $INC/large`
+
+	LARGE=0
+	if [ -e $INC/large ]; then
+	  LARGE=1
+	fi
 
 	echo ""
 	echo "Root and quality ..."

diff --git a/phylogeny/distTree_inc_calibrate.sh b/phylogeny/distTree_inc_calibrate.sh
@@ -23,12 +23,11 @@ $THIS/makeDistTree  -threads 15  -data $INC/  -variance $VARIANCE  -dissim_coeff
 
 echo ""
 echo ""
-LARGE=`cat $INC/large`
-LARGE_PAR=""
-if [ $LARGE == 1 ]; then
-  LARGE_PAR="-large"
+LARGE=""
+if [ -e $INC/large ]; then
+  LARGE="-large"
 fi
-$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree  -features $INC/phen  $LARGE_PAR \
+$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree  -features $INC/phen  $LARGE \
   -prefer_gain  -nominal_singleton_is_optional  -qual $TMP.qual   -output_core $TMP.core  -save_mem
 
 

diff --git a/phylogeny/distTree_inc_complete.sh b/phylogeny/distTree_inc_complete.sh
@@ -102,7 +102,10 @@ cp $INC/tree $INC/hist/tree.1
 if [ -e $INC/phen ]; then
   echo ""
   echo "Quality ..."
-	LARGE=`cat $INC/large`
+  LARGE=0
+  if [ -e $INC/large ]; then
+    LARGE=1
+  fi
   $THIS/tree_quality_phen.sh $INC/tree "" $INC/phen $LARGE 0 "" > $INC/hist/tree_quality_phen.1
 	grep ' !' $INC/hist/tree_quality_phen.1
 fi

diff --git a/phylogeny/distTree_inc_init.sh b/phylogeny/distTree_inc_init.sh
@@ -78,11 +78,18 @@ echo "$VARIANCE"          > $INC/variance
 echo $DISSIM_BOUNDARY     > $INC/dissim_boundary
 echo $GENOGROUP_BARRIER   > $INC/genogroup_barrier
 echo $HYBRIDNESS_MIN      > $INC/hybridness_min
-echo $LARGE               > $INC/large
-echo $REQUEST_CLOSEST_SQL > $INC/request_closest_sql
 echo $SERVER              > $INC/server
 echo $DATABASE            > $INC/database
 
+if [ $LARGE == 1 ]; then
+  touch $INC/large
+fi
+
+if [ $REQUEST_CLOSEST_SQL == 1 ]; then
+  touch $INC/request_closest_sql
+fi
+
+
 
 function create_script
 {

diff --git a/phylogeny/distTree_inc_new.sh b/phylogeny/distTree_inc_new.sh
@@ -18,7 +18,6 @@ GRID_MIN=`cat $INC/grid_min`
 QC=""  # -qc  
 RATE=0.015   # PAR
 VARIANCE=`cat $INC/variance`
-REQUEST_CLOSEST_SQL=`cat $INC/request_closest_sql`
 OBJS=`$THIS/tree2obj.sh $INC/tree | wc -l`
 ADD=`echo "$OBJS * $RATE" | bc -l | sed 's/\..*$//1'`  # PAR
 if [ $ADD == 0 ]; then
@@ -89,7 +88,7 @@ if [ $N -gt 0 ]; then
   else
     $THIS/../grid_wait.sh 1
     UL1=""
-    if [ $REQUEST_CLOSEST_SQL == 1 ]; then
+    if [ -e $INC/request_closest_sql ]; then
       UL1=",ul1=30"
     fi
     $THIS/../trav  -step 1  $INC/search "$QSUB_5$UL1  -N j%n  %Q$THIS/distTree_inc_search_init.sh $INC %f%Q > /dev/null" 

diff --git a/phylogeny/distTree_inc_new_cmd.sh b/phylogeny/distTree_inc_new_cmd.sh
@@ -14,8 +14,7 @@ LIST=$3
 
 
 H=""
-LARGE=`cat $INC/large`
-if [ $LARGE == 1 ]; then
+if [ -e $INC/large ]; then
   H="%h/"
 fi
 

diff --git a/phylogeny/distTree_inc_new_list.sh b/phylogeny/distTree_inc_new_list.sh
@@ -9,8 +9,7 @@ fi
 INC=$1
 
 
-LARGE=`cat $INC/large`
-if [ $LARGE == 1 ]; then
+if [ -e $INC/large ]; then
   N=`ls $INC/new | wc -l`
   if [ $N -ne 1000 ]; then
     error "$INC/new/ has no 1000 subdirectories (it has $N)"

diff --git a/phylogeny/distTree_inc_optimize.sh b/phylogeny/distTree_inc_optimize.sh
@@ -26,6 +26,9 @@ $THIS/makeDistTree  -threads 15  -data $INC/  -variance $PAR  -optimize  -skip_l
 
 echo ""
 echo "Quality ..."
-LARGE=`cat $INC/large`
+LARGE=0
+if [ -e $INC/large ]; then
+  LARGE=1
+fi
 $THIS/tree_quality_phen.sh $OUT_TREE "" $INC/phen $LARGE 1 ""
 
diff --git a/phylogeny/distTree_inc_tree1_quality.sh b/phylogeny/distTree_inc_tree1_quality.sh
@@ -18,7 +18,10 @@ echo ""
 echo "Quality of the initial tree ..."
 VER=`cat $INC/version`
 $THIS/tree2obj.sh $INC/hist/tree.1 > $INC/_init.list
-LARGE=`cat $INC/large`
+LARGE=0
+if [ -e $INC/large ]; then
+  LARGE=1
+fi
 $THIS/tree_quality_phen.sh $INC/tree $INC/_init.list $INC/phen $LARGE 0 "" > $INC/hist/makeFeatureTree-tree1.$VER
 rm $INC/_init.list
 grep ' !' $INC/hist/makeFeatureTree-tree1.$VER

diff --git a/phylogeny/distTree_inc_tree1_quality_hist.sh b/phylogeny/distTree_inc_tree1_quality_hist.sh
@@ -21,7 +21,10 @@ echo $TMP > /dev/stderr
 VER=`cat $INC/version`
 echo $VER > /dev/stderr
 $THIS/tree2obj.sh $INC/hist/tree.1 > $TMP.init
-LARGE=`cat $INC/large`
+LARGE=0
+if [ -e $INC/large ]; then
+  LARGE=1
+fi
 $THIS/tree2obj.sh $INC/tree > $TMP.last
 $THIS/../setIntersect.sh $TMP.init $TMP.last 0 > $TMP.list
 

diff --git a/phylogeny/distTree_inc_unsearch.sh b/phylogeny/distTree_inc_unsearch.sh
@@ -12,8 +12,7 @@ OBJ=$2
 
 
 H=""
-LARGE=`cat $INC/large`
-if [ $LARGE == 1 ]; then
+if [ -e $INC/large ]; then
   H=`$THIS/../file2hash $OBJ`
   H="$H/"
 fi

diff --git a/version.inc b/version.inc
@@ -1,6 +1,7 @@
-#define VERSION "1.3.2"
+#define VERSION "1.4.1"
 
 
+// 1.4.1  01/24/2021  inc/{large,request_closest_sql} /dev/null or absent
 // 1.3.2  01/10/2021  GeneMark2CDS prints incomplete and ambiguous proteins as well
 // 1.3.1  12/18/2020  inc/phen_large --> inc/large; inc/request_closest_sql
 // 1.2.3  10/03/2020  makeDistTree does not stop on criterion increase of dissimilarity types > 1
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,8 +14,7 @@ LIST=$3 @@
     H=""
-    LARGE=`cat $INC/large`
-    if [ $LARGE == 1 ]; then
+    if [ -e $INC/large ]; then
       H="%h/"
     fi
@@ Expand Down @@