Problem2Attempt

## Problem 2 ##

#Load Libraries

library(regexr)

#Reading data into an object

readData=scan(file="motifsort.fasta", what = "charecter")

#Convert object to a vector
vectorData=data.frame(readData)

#Create output files

file.create("motif1")
file.create("motif2")
file.create("unknown")

#for loop filtering out sequence desgination lines
for (i in vectorData[,1]){
  
}
#for loop to search for motifs and sort
for(i in data[,1]){
  if(grepl("AKKPRVZE", data[i,1])){
    
    write(data[i,1], file = "motif1", append = TRUE)
  } else {if (grepl("AAQWWRNYGG", data[i,1])){
    
    write(data[i,1], file = "motif2", append = TRUE)
} else { if (!grepl("sequence", data[i,1])){
  
  write(data[i,1], file = "unknown", append = TRUE)
}}
  }}


#attempts to add the sequence number in front of the sequences sorted into the different motif files (these are removed from the if loop to try and troubleshoot)
write(data[(i-1),1], file = "motif1", append= TRUE)
write(data[(i-1),1], file = "motif2", append= TRUE)    
write(data[(i-1),1], file = "unknown", append= TRUE)