I'm trying to calculate "PSSM feature" using protr package. I tried to adapt the example in the documentation to fit my data, but I always get an error.
Here is my code:
x <- readFASTA('P08195.fasta')[] dbpath <- tempfile("tempdb", fileext = ".fasta") invisible(file.copy(from = system.file('P08195.fasta'),to = dbpath) ) pssmmat <- extractPSSM(seq = x, database.path = dbpath) pssmfeature <- extractPSSMFeature(pssmmat) head(pssmfeature)
Here is the error message:
Warning message in readLines(file): "incomplete final line found on 'P08195.fasta'" Warning message in file(con, "r"): "cannot open file 'C:\Users\Adham\AppData\Local\Temp\RtmpaGM54r\protrPSIBlast433023ad2ce8.pssm': No such file or directory" Error in file(con, "r"): cannot open the connection Traceback: 1. extractPSSM(seq = x, database.path = dbpath) 2. readLines(PSSMfile) 3. file(con, "r")
I'm not so familiar with R since I use Python mainly. How can I solve this issue?