func init() {
runtime.GOMAXPROCS(runtime.NumCPU())
util.FlagUse("cpu")
util.FlagParse("database-path frag-lib-dir query-pdb-file "+
"[query-pdb-file ...]", "")
util.AssertLeastNArg(2)
}
func init() {
util.FlagParse(
"out-file matrix-file [ matrix-file ... ]",
"Combines the input matrices into a 'best-of-all' matrix by\n"+
"using the best (lowest) SAS score for each pair. All given\n"+
"matrices must be exactly the same size.")
util.AssertLeastNArg(2)
}
func init() {
flag.IntVar(&flagRandoms, "n", flagRandoms,
"The number of random permutations to use.")
util.FlagUse("cpu", "cpuprof")
util.FlagParse(
"out-file vectors-csv 'comma-sep-cath-domains' ...",
"Computes the probability that each cluster of cath domains is\n"+
"significantly different with respect to their Fragbag vectors.")
util.AssertLeastNArg(3)
}
func init() {
flag.StringVar(&flagFragbag, "fragbag", "fragbag",
"The old fragbag executable.")
flag.BoolVar(&flagOldStyle, "oldstyle", false,
"When true, PDB chains will be concatenated together as if they were "+
"one chain to compute a BOW vector.")
util.FlagParse(
"library-file brk-file pdb-file [pdb-file ...]",
"Note that if the old library and the new library don't have the\n"+
"same number of fragments and the same fragment size, bad things\n"+
"will happen.\n")
util.AssertLeastNArg(3)
}
func init() {
flag.Float64Var(&flagThreshold, "threshold", flagThreshold,
"Set the distance threshold to use when computing AUC.")
util.FlagUse("cpu", "cpuprof")
util.FlagParse(
"cath-domain-labels best-of-all-matrix"+
"(bowdb | matrix-file) out-file "+
"[ (bowdb | matrix-file) out-file ... ]",
"Computes the AUC of each aligner matrix (or BOW database) given\n"+
"with respect to the 'best-of-all' matrix given. Each AUC is\n"+
"written to a separate out-file. The sizes of all matrices must\n"+
"be exactly equivalent.\n"+
"Files are interpreted as BOW databases if they have a '.bowdb'\n"+
"file extension.")
util.AssertLeastNArg(4)
if util.NArg()%2 != 0 {
util.Fatalf("There must be an out file for each matrix or bowdb file.")
}
}
func init() {
u := "fraglib pdb-file [ chain-id [ start stop ] ]"
util.FlagParse(u, "")
util.AssertLeastNArg(2)
}
func init() {
util.FlagUse("cpu", "seq-db", "pdb-hhm-db", "blits", "verbose",
"hhfrag-min", "hhfrag-max", "hhfrag-inc")
util.FlagParse("out-dir target-fasta", "")
util.AssertLeastNArg(2)
}