changeset 6:0bc169bae3a1 draft default tip

Uploaded
author jfb
date Thu, 19 Apr 2018 17:23:14 -0400
parents 1475ecc69c9e
children
files promap/last.dump.rda promap/promap.R promap/promap.xml promap/test-data/Unshared Coulambic Data.csv promap/test-data/Unshared LJ Data.csv
diffstat 5 files changed, 2287 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
Binary file promap/last.dump.rda has changed
--- a/promap/promap.R	Thu Apr 19 13:20:19 2018 -0400
+++ b/promap/promap.R	Thu Apr 19 17:23:14 2018 -0400
@@ -1,13 +1,13 @@
-options(error = quote({
-  dump.frames(to.file=T, dumpto='last.dump')
-  load('last.dump.rda')
-  print(last.dump)
-  q()
-}))
+# options(error = quote({
+#   dump.frames(to.file=T, dumpto='last.dump')
+#   load('last.dump.rda')
+#   print(last.dump)
+#   q()
+# }))
 
 #symdiff <- function( x, y) { setdiff( union(x, y), intersect(x, y))}
 
-options(error = quote({dump.frames(to.file=TRUE); q()}))
+# options(error = quote({dump.frames(to.file=TRUE); q()}))
 
 CoulambicOutput<-"CoulambicOutput.csv"
 LJoutput<-"LJOutput.csv"
@@ -16,9 +16,10 @@
 #print(args)
 
 myinput <- gsub("--in=", "", args[grepl("--in=", args)])
-# #input<-list(read.fwf(file = "1-finedata.txt", widths=c(4,5,4,6,6,4,5,6,12,12,12)),read.fwf(file = "2-finedata.txt", widths=c(4,5,4,6,6,4,5,6,12,12,12)))
 input<-lapply(myinput, function(x){read.fwf(file = x, widths=c(4,5,4,6,6,4,5,6,12,12,12))})
 
+#input<-list(read.fwf(file = "1-finedata.txt", widths=c(4,5,4,6,6,4,5,6,12,12,12)),read.fwf(file = "2-finedata.txt", widths=c(4,5,4,6,6,4,5,6,12,12,12)))
+
 #print("hi")
 
 #myinput <- gsub("--in=", "", args[grepl("--in=", args)])
@@ -158,6 +159,12 @@
 combinedCoul<-c()
 CombinedLJ<-c()
 
+UnsharedLJData<-list()
+UnsharedLJPositions<-list()
+
+UnsharedCoulData<-list()
+UnsharedCoulPositions<-list()
+
 for (z in 1:length(ListOfMine)) {
   DamnThatDataIsFine<-ListOfMine[z]
   DamnThatDataIsFine<-as.data.frame(DamnThatDataIsFine)
@@ -201,6 +208,32 @@
   #these z ifs create the intersection to find only which LJ and Coul vals were shared between the things, then I just need to extract the
   #positional values of those
   #SO THESE ARE THE FULL NAMES OF THE SHARED VALUES, NO THEIR POSITIONAL MATRIX VALUES
+  if (z==length(ListOfMine)){
+    for (w in 1:length(ListOfMine)) {
+      #setdif(x,y) means "what does x have that y doesn't?"
+      #in this loop I am taking the set difference of each input set, the difference between them and the union set created in the previous if
+      ThisData<-ListOfMine[w]
+      ThisData<-as.data.frame(ThisData)
+      ComparableData<-ThisData[,c(1,2,3,5,6,7)]
+      ComparableData<-apply(ComparableData,1,paste,collapse=" ")
+      
+      #so I think I'm going to do this the stupid but easy way.  I will perform the setdif function.  Then I will perform a function to see 
+      #which positions are the different ones, then save those positions
+      #currently this includes BOTH THOSE THAT WERE < THE VALUE AND THOSE THAT WERE >VALUE BUT UNSHARED
+      TheseUnsharedCoul<-setdiff(ComparableData,combinedCoul)
+      TheseUnsharedLJ<-setdiff(ComparableData,CombinedLJ)
+      
+      CoulUnsharedPositions<-match(TheseUnsharedCoul,ComparableData)
+      LJUnsharedPositions<-match(TheseUnsharedLJ,ComparableData)
+      
+      UnsharedLJData[[w]]<-ThisData[LJUnsharedPositions,c(1,2,3,5,6,7,9,11)]
+      UnsharedLJPositions[[w]]<-LJUnsharedPositions
+      
+      UnsharedCoulData[[w]]<-ThisData[CoulUnsharedPositions,c(1,2,3,5,6,7,9,10)]
+      UnsharedCoulPositions[[w]]<-CoulUnsharedPositions
+      #AA1 AA# Atom Atom# AA2 AA2# Atom2 Atom2# Dist Coul LJ
+    }
+  }
 }
 
 
@@ -315,5 +348,42 @@
 
 
 
-#I think I just won't tell Oscar
-#could put this on GalaxyP as 10 programs, each one firing for a different amount of inputs
\ No newline at end of file
+
+# UnsharedLJData<-list()
+# UnsharedLJPositions<-list()
+# 
+# UnsharedCoulData<-list()
+# UnsharedCoulPositions<-list()
+
+
+
+name<-"UnsharedCoulambicData.csv"
+name2<-"UnsharedLJData.csv"
+
+
+Header<-rep(" ",times=8)
+CoulHead<-c("First Amino Acid","First AA Number","First Atom Name","Second Amino Acid","Second AA Number","Second Atom Name","Distance","Coulambic Value")
+LJHead<-c("First Amino Acid","First AA Number","First Atom Name","Second Amino Acid","Second AA Number","Second Atom Name","Distance","LJ Value")
+
+CoulHead<-rbind(Header,CoulHead)
+LJHead<-rbind(Header,LJHead)
+
+write.table(x=CoulHead,file = name,row.names = FALSE,col.names = FALSE,append = TRUE,sep = ",")
+write.table(x=LJHead,file = name2,row.names = FALSE,col.names = FALSE,append = TRUE,sep = ",")
+
+for (g in 1:length(UnsharedCoulData)) {
+  Seperator<-"Input Number "
+  Seperator<-paste0(Seperator,g)
+  
+  write.table(x=Seperator,file = name,sep = ",",row.names = FALSE,col.names = FALSE,append = TRUE)
+  write.table(x=Seperator,file = name2,sep = ",",row.names = FALSE,col.names = FALSE,append = TRUE)
+  
+  LJdata<-UnsharedLJData[g]
+  LJdata<-as.data.frame(LJdata)
+  
+  CoulData<-UnsharedCoulData[g]
+  CoulData<-as.data.frame(CoulData)
+  
+  write.table(x=CoulData,file = name,sep = ",",row.names = FALSE,col.names = FALSE,append = TRUE)
+  write.table(x=LJdata,file = name2,sep = ",",row.names = FALSE,col.names = FALSE,append = TRUE)
+}
--- a/promap/promap.xml	Thu Apr 19 13:20:19 2018 -0400
+++ b/promap/promap.xml	Thu Apr 19 17:23:14 2018 -0400
@@ -19,6 +19,8 @@
     <outputs>
         <data format="csv" name="CoulOutputs" from_work_dir="CoulambicOutput.csv" label="Coulombic Output.csv"/>
         <data format="csv" name="LJOutputs" from_work_dir="LJOutput.csv" label="LJ Output.csv"/>
+		<data format="csv" name="UnsharedCoulOutputs" from_work_dir="UnsharedCoulambicData.csv" label="Unshared Coulombic Output.csv"/>
+        <data format="csv" name="UnsharedLJOutputs" from_work_dir="UnsharedLJData.csv" label="Unshared LJ Output.csv"/>
     </outputs>
     <tests>
         <test>
@@ -31,9 +33,6 @@
 
     
     <help><![CDATA[
-		Promap is something that I should ask Oscar about what it is and what its purpose is
+		Promap looks at atom-atom interactions that were discovered by OpenContant, and it gives to the user which interactions where shared and which were not between multiple snapshots or multiple isoforms
     ]]></help>
-    <citations>
-        <citation type="doi">10.1021/ja507164a</citation>
-    </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/promap/test-data/Unshared Coulambic Data.csv	Thu Apr 19 17:23:14 2018 -0400
@@ -0,0 +1,621 @@
+" "," "," "," "," "," "," "," "
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/promap/test-data/Unshared LJ Data.csv	Thu Apr 19 17:23:14 2018 -0400
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