diff NMF/NMF.R @ 0:dd301fc4b54e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NMF/NMF.R	Fri Feb 23 16:37:29 2018 -0500
@@ -0,0 +1,180 @@
+NAMEOFOUTPUTFILE<-"output1.csv"
+#this is the name of the file you will create
+
+
+
+SuperAwesometrial <- read.delim2("input1.tabular", header=FALSE)
+#once you've used the other script to turn the FASFA into a CSV, copypaste the filepath and name 
+#of the csv into this line between the quote marks.  
+
+SBF<-read.csv("input3.csv", stringsAsFactors = FALSE)
+  
+
+PositiveMotifs <- read.csv("input2.csv", stringsAsFactors=FALSE)
+#because of R reasons, it is required that the motifs in this file have blank cells instead of spaces where there is no letter in 
+#the motif
+
+################################################################################################################################
+#I have to paste them, then split and unlist them, then find the x and paste again
+Positive9Letters<-PositiveMotifs[,4:18]
+#head(Positive9Letters)
+PositiveTrueMotifs<-c()
+
+AccessionNumbers<-SBF[,1]
+ALLPOSSIBLE<-SuperAwesometrial[,1]
+ALLPOSSIBLE<-as.character(ALLPOSSIBLE)
+################################################################################################################################
+
+for (q in 1:nrow(Positive9Letters)) {
+  LeftJust<-0
+  RightJust<-0
+  
+  motifmotif<-Positive9Letters[q,]
+  motifmotif<-paste(motifmotif, collapse = "",sep = "")
+  
+  motifmotif<-unlist(strsplit(motifmotif, split = ""))
+  
+  position <- match(x = "x", table = motifmotif)
+  LeftJust<-position-1
+  RightJust<-length(motifmotif)-position-1
+  
+  LeftSpaces<-rep(x=" ", times=(7-LeftJust))
+  RightSpaces<-rep(x=" ", times=(7-RightJust))
+  
+  motifmotif<-motifmotif[!motifmotif %in% c("x")]
+  
+  motifmotif<-c(LeftSpaces,motifmotif,RightSpaces)
+  motifmotif<-paste(motifmotif, collapse = "",sep = "")
+  PositiveTrueMotifs<-c(PositiveTrueMotifs,motifmotif)
+}
+
+
+################################################################################################################################
+allmotifs<-matrix(data=c("Motifs"),nrow=1)
+thenames<-matrix(data=c("AccessionNumbers"),nrow = 1)
+################################################################################################################################
+
+################################################################################################################################
+
+#TrueMotifNums<-which(ALLPOSSIBLE %in% AccessionNumbers)
+#fihlodeANs<-c()
+for (q in 1:length(AccessionNumbers)) {
+  patterno<-AccessionNumbers[q]
+  location<-sapply(ALLPOSSIBLE, grepl, pattern=patterno, fixed=TRUE)
+  if (sum(location)>0){
+    whereisit<-which(location %in% TRUE)
+    for (u in 1:length(whereisit)) {
+      i<-whereisit[u]
+      name<-c()
+      data<-c()
+      name<-as.character(SuperAwesometrial[i,1])
+      #the name of each protein is the first column 
+      name<-sub(x=name, pattern=",", replacement="")
+      #the names may contain commas, remove them
+      data<-as.character(SuperAwesometrial[i,3])
+      #the amino acids are stored in the third column
+      data<-strsplit(data,"")
+      #split them into their component letters
+      data<-unlist(data)
+      #turn them into a vector
+      motif<-c()
+      for (j in 1:length(data)){
+        if ("Y" %in% data[j]){
+          #if there is a Y aka Tyrosine in the data
+          #allmotifs=rbind(allmotifs,data[(i-4):(i+4)])
+          a<-j-7
+          if (a<1){
+            a<-1
+          }
+          b<-j+7
+          if (b>length(data)){
+            b<-length(data)
+          }
+          #take the motif that is +/- 4 from that Y, sanity checks so that values are never off the grid from the protein
+          
+          LeftSide<-7-(j-a)
+          RightSide<-7-(b-j)
+          #how is the motif justified?  Does it have exactly 4 letters to the left/right, or does it not?
+          
+          leftspaces<-rep(" ",times=LeftSide)
+          rightspaces<-rep(" ",times=RightSide)
+          #add blank spaces if the motif has less than 4 letters to the left/right
+          
+          
+          motif<-(data[(a):(b)])
+          motif<-c(leftspaces,motif,rightspaces)
+          #save that motif, which is the Y and +/- 4 amino acids, including truncation
+          
+          # lens<-c(lens,length(motif))
+          # leni<-c(leni,i)
+          # lenj<-c(lenj,j)
+          
+          motif<-paste(motif, sep="", collapse="")
+          #the 4 amino acids, put them back together into a single string
+          motif<-matrix(data=c(motif),nrow = 1)
+          namesss<-matrix(data=c(name),nrow = 1)
+          #keep this motif and separately keep the name of the protein it came from
+          allmotifs<-rbind(allmotifs,motif)
+          thenames<-rbind(thenames,namesss)
+          #add names and motifs to a growing list
+          
+          # write.table(motif, file="TRIALTIALRIAALSKFDJSD.csv", quote=FALSE, sep=",",
+          #             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
+          #and then write it into a csv, the sep is needed so that the two pieces of the data frame are separated
+          #append has 1to equal true because this thing will loop around many times adding more and more data points
+          #you must create a new filename/filepath with each new data you run
+        }
+      }
+    }
+  }
+}
+
+
+
+
+################################################################################################################################
+################################################################################################################################
+################################################################################################################################
+
+
+# for (i in 1:nrow(SuperAwesometrial)){
+# 
+# }
+
+names(allmotifs)<-thenames
+
+truemotifs<-allmotifs[!duplicated(allmotifs)]
+#truenames<-thenames[!duplicated(thenames)]
+#remove duplicates from the motifs and names
+
+#make the motifs and names into matrices
+
+# for (w in 1:nrow(truemotifs)) {
+#   for (e in 1:length(PositiveTrueMotifs)){
+#     if (grepl(pattern=PositiveTrueMotifs[e], x=truemotifs[w,1],ignore.case = TRUE)==TRUE){
+#       truemotifs[w,1]<-NA
+#     }
+#   }
+# }
+
+truemotifs<-truemotifs[!truemotifs %in% PositiveTrueMotifs]
+
+# truemotifs<-matrix(data = truemotifs,ncol = 1)
+# truenames<-matrix(data=truenames,ncol = 1)
+# 
+# 
+# #program only works if there are more motifs than names, fuck it
+# 
+# rowsrows<-nrow(truemotifs)-nrow(truenames)
+# nanas<-rep(NA,times=rowsrows)
+# nanas<-matrix(data = nanas,ncol = 1)
+# truenames<-rbind(truenames,nanas)
+# #to turn the motifs and names into a single output matrix, add enough rows of NAs so the two initial matrices are equivalent,
+# #then put them together columnwise
+
+outputfile<-cbind(names(truemotifs),truemotifs)
+
+outputfile <- gsub(",","",outputfile)
+
+write.table(outputfile, file=NAMEOFOUTPUTFILE, quote=FALSE, sep=",",
+             row.names=FALSE,col.names = FALSE, na="", append=TRUE)