Exemplo n.º 1
0
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)
}
Exemplo n.º 2
0
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)
}
Exemplo n.º 3
0
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)
}
Exemplo n.º 4
0
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)
}
Exemplo n.º 5
0
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.")
	}
}
Exemplo n.º 6
0
func init() {
	u := "fraglib pdb-file [ chain-id [ start stop ] ]"
	util.FlagParse(u, "")
	util.AssertLeastNArg(2)
}
Exemplo n.º 7
0
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)
}