Mercurial > repos > jfb > promap
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
--- 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>
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