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.FlagUse("cpu")
util.FlagParse("frag-lib-dir chain pdb-file out-bow",
"Computes and outputs a BOW file for the specified chain in the\n"+
"given PDB file. If 'out-bow' is '--', then a human readable\n"+
"version of the BOW will be printed to stdout instead.")
util.AssertNArg(4)
}
func init() {
flag.BoolVar(&flagQuiet, "quiet", flagQuiet,
"When set, hhblits/hhmake output will be hidden.")
util.FlagUse("seq-db")
util.FlagParse("in-fasta-file out-hhm-file", "")
util.AssertNArg(2)
}
func init() {
flag.Float64Var(&flagRmsd, "rmsd", flagRmsd,
"The RMSD cut-off to use to determine true positives.")
util.FlagUse("pdb-dir")
util.FlagParse("fmap-file", "")
util.AssertNArg(1)
}
func init() {
flag.IntVar(&flagNum, "n", flagNum, "The number of PDB entries to echo.")
flag.BoolVar(&flagPaths, "paths", flagPaths,
"When set, full file paths will be echoed instead of PDB ids.")
util.FlagUse("pdb-dir")
util.FlagParse("", "")
rand.Seed(time.Now().UnixNano())
}
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.Float64Var(&flagThreshold, "threshold", flagThreshold,
"The threshold at which to cut the tree.")
flag.StringVar(&flagGobIt, "gobit", flagGobIt,
"If set, alignment distances will be cached to the file given, "+
"then mattbench-cluster will quit.")
util.FlagUse("cpu", "cpuprof", "verbose")
util.FlagParse(
"(astral-alignment-dir | alignment-distances-gob) dendrogram-tree "+
"out-clusters.csv",
"Where `dendrogram-tree` is a file in Newick tree format.")
if len(flagGobIt) > 0 {
util.AssertNArg(1)
} else {
util.AssertNArg(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() {
util.FlagUse("cpu")
util.FlagParse("frag-lib-dir fmap-file out-bow", "")
util.AssertNArg(3)
}
func init() {
util.FlagUse("cpu", "seq-db", "pdb-hhm-db", "blits",
"hhfrag-min", "hhfrag-max", "hhfrag-inc")
util.FlagParse("target-fasta out-fmap", "")
util.AssertNArg(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)
}