Like most informatics throughput methods, epitope prediction generates a lot of output and in a not so friendly format suitable for subsequent analysis. I considered writing a parser for the output using Ruby, but would that not take long? A simple vim function that I added to my .vimrc file to format the output and use a single keystroke worked the magic and saved time.
" formating output from netMHCII-pan program function! FormatNetmhcOutput() g/^\#/norm dd g/^--/norm dd g/^Protein/norm dd %le g/^pos/norm dd %s/<=\sWB//g %s/<=\sSB//g %s/\s\+$// %s/\s\+/,/g g/^$/d endfunction nmap ;h :call FormatNetmhcOutput()
This function can be called by pressing the ; and h key when in normal mode. It removes comments and provides a csv output that can be read with a simple R directive.
data <– read.csv("file.csv")