Website for calculating CRAP of given proteome
Parameters:
"-0j #" - Set minimum complexity (default .9) "-ct #" - Set threshold for running CD-HIT (default .7) "-cl #" - Set fractional length for redundancy filtering (default .8) "-min #" - Set minimum length (default 30) "-max #" - Set maximum length (default 30000) "-fft #" - Set threshold for running CD-HIT in Fusion/Fission filter (default .7) "-ffl #" - Set fractional length (bottom) for fusion/fission filtering (default .8) "-xs #" - Maximum number of consecutive Xs in sequence to ignore (default 0) "-ms" - Check for M as first amino acid (default does not check) "-nolen" - Destage length filter (default completes stage) "-nocomp" - Destage complexity (0j) filter (default completes stage) "-nored" - Destage redundancy (CD-HIT) filter (default completes stage) "-noff" - Destage fusion/fission (Ff) filter (default completes stage)
Command Example:
bash$> python process_crap.py [input] [clean_output] [messy_output] [email] [parameters]