# HG changeset patch
# User jfb
# Date 1519833681 18000
# Node ID 891f465be772dc9231bf196d168836a559581d40
# Parent  d5e9648231470c6a331235aef4b7bc0b3b4b68a9
Uploaded

diff -r d5e964823147 -r 891f465be772 kinatestid_r/Kinatest-R.R
--- a/kinatestid_r/Kinatest-R.R	Wed Feb 28 10:53:29 2018 -0500
+++ b/kinatestid_r/Kinatest-R.R	Wed Feb 28 11:01:21 2018 -0500
@@ -1153,6 +1153,40 @@
 bareSDs<-SDtable[2:21,2:16]
 goodones<-bareSDs>2
 
+# Positionm7<-which(goodones[,1] %in% TRUE)
+# if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
+# Positionm6<-which(goodones[,2] %in% TRUE)
+# if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
+# Positionm5<-which(goodones[,3] %in% TRUE)
+# if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
+# Positionm4<-which(goodones[,4] %in% TRUE)
+# if (length(Positionm4)<2){Positionm4<-bareSDs[,4][order(bareSDs[,4])[1:2]]}
+# Positionm3<-which(goodones[,5] %in% TRUE)
+# if (length(Positionm3)<2){Positionm3<-bareSDs[,5][order(bareSDs[,5])[1:2]]}
+# Positionm2<-which(goodones[,6] %in% TRUE)
+# if (length(Positionm2)<2){Positionm2<-bareSDs[,6][order(bareSDs[,6])[1:2]]}
+# Positionm1<-which(goodones[,7] %in% TRUE)
+# if (length(Positionm1)<2){Positionm1<-bareSDs[,7][order(bareSDs[,7])[1:2]]}
+# 
+# Positiond0<-which(goodones[,8] %in% TRUE)
+# if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
+# 
+# Positionp1<-which(goodones[,9] %in% TRUE)
+# if (length(Positionp1)<2){Positionp1<-bareSDs[,9][order(bareSDs[,9])[1:2]]}
+# Positionp2<-which(goodones[,10] %in% TRUE)
+# if (length(Positionp2)<2){Positionp2<-bareSDs[,10][order(bareSDs[,10])[1:2]]}
+# Positionp3<-which(goodones[,11] %in% TRUE)
+# if (length(Positionp3)<2){Positionp3<-bareSDs[,11][order(bareSDs[,11])[1:2]]}
+# Positionp4<-which(goodones[,12] %in% TRUE)
+# if (length(Positionp4)<2){Positionp4<-bareSDs[,12][order(bareSDs[,12])[1:2]]}
+# Positionp5<-which(goodones[,13] %in% TRUE)
+# if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
+# Positionp6<-which(goodones[,14] %in% TRUE)
+# if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
+# Positionp7<-which(goodones[,15] %in% TRUE)
+# if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
+
+
 Positionm7<-which(goodones[,1] %in% TRUE)
 if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
 Positionm6<-which(goodones[,2] %in% TRUE)
@@ -1160,25 +1194,25 @@
 Positionm5<-which(goodones[,3] %in% TRUE)
 if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
 Positionm4<-which(goodones[,4] %in% TRUE)
-if (length(Positionm4)<2){Positionm4<-bareSDs[,4][order(bareSDs[,4])[1:2]]}
+if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
 Positionm3<-which(goodones[,5] %in% TRUE)
-if (length(Positionm3)<2){Positionm3<-bareSDs[,5][order(bareSDs[,5])[1:2]]}
+if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
 Positionm2<-which(goodones[,6] %in% TRUE)
-if (length(Positionm2)<2){Positionm2<-bareSDs[,6][order(bareSDs[,6])[1:2]]}
+if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
 Positionm1<-which(goodones[,7] %in% TRUE)
-if (length(Positionm1)<2){Positionm1<-bareSDs[,7][order(bareSDs[,7])[1:2]]}
+if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
 
 Positiond0<-which(goodones[,8] %in% TRUE)
 if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
 
 Positionp1<-which(goodones[,9] %in% TRUE)
-if (length(Positionp1)<2){Positionp1<-bareSDs[,9][order(bareSDs[,9])[1:2]]}
+if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
 Positionp2<-which(goodones[,10] %in% TRUE)
-if (length(Positionp2)<2){Positionp2<-bareSDs[,10][order(bareSDs[,10])[1:2]]}
+if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
 Positionp3<-which(goodones[,11] %in% TRUE)
-if (length(Positionp3)<2){Positionp3<-bareSDs[,11][order(bareSDs[,11])[1:2]]}
+if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
 Positionp4<-which(goodones[,12] %in% TRUE)
-if (length(Positionp4)<2){Positionp4<-bareSDs[,12][order(bareSDs[,12])[1:2]]}
+if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
 Positionp5<-which(goodones[,13] %in% TRUE)
 if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
 Positionp6<-which(goodones[,14] %in% TRUE)
@@ -1186,40 +1220,6 @@
 Positionp7<-which(goodones[,15] %in% TRUE)
 if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
 
-
-# Positionm7<-which(goodones[,1] %in% TRUE)
-# if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
-# Positionm6<-which(goodones[,2] %in% TRUE)
-# if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
-# Positionm5<-which(goodones[,3] %in% TRUE)
-# if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
-# Positionm4<-which(goodones[,4] %in% TRUE)
-# if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
-# Positionm3<-which(goodones[,5] %in% TRUE)
-# if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
-# Positionm2<-which(goodones[,6] %in% TRUE)
-# if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
-# Positionm1<-which(goodones[,7] %in% TRUE)
-# if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
-# 
-# Positiond0<-which(goodones[,8] %in% TRUE)
-# if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
-# 
-# Positionp1<-which(goodones[,9] %in% TRUE)
-# if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
-# Positionp2<-which(goodones[,10] %in% TRUE)
-# if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
-# Positionp3<-which(goodones[,11] %in% TRUE)
-# if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
-# Positionp4<-which(goodones[,12] %in% TRUE)
-# if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
-# Positionp5<-which(goodones[,13] %in% TRUE)
-# if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
-# Positionp6<-which(goodones[,14] %in% TRUE)
-# if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
-# Positionp7<-which(goodones[,15] %in% TRUE)
-# if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
-
 # Positionm7<-which(goodones[,1] %in% TRUE)
 # if (length(Positionm7)<3){Positionm7<-bareSDs[,1][order(bareSDs[,1])[1:3]]}
 # Positionm6<-which(goodones[,2] %in% TRUE)
diff -r d5e964823147 -r 891f465be772 kinatestid_r/kinatestid_r.xml
--- a/kinatestid_r/kinatestid_r.xml	Wed Feb 28 10:53:29 2018 -0500
+++ b/kinatestid_r/kinatestid_r.xml	Wed Feb 28 11:01:21 2018 -0500
@@ -40,7 +40,7 @@
 Important!
 **Please write the name of your kinase in ALL CAPS so the R script can recognize it!  Thank you!**
 **If your kinase is one of the following kinases, please use this form of its name:  ABL, ARG, BTK, CSK, FYN, HCK, JAK2, LCK, LYN, PYK2, SRC, SYK, YES, FLT3**
-**So for example if your kinase is ARG please use ARG and not ABL2
+**So for example if your kinase is ARG please use ARG and not ABL2**
 	
 This tool is intended for use in conjunction with KinaMine.jar and Negative Motif Finder.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates