Exemple #1
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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)
}
Exemple #2
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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)
}
Exemple #3
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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)
}
Exemple #4
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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)
}
Exemple #5
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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())
}
Exemple #6
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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)
}
Exemple #7
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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)
	}
}
Exemple #8
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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.")
	}
}
Exemple #9
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func init() {
	util.FlagUse("cpu")
	util.FlagParse("frag-lib-dir fmap-file out-bow", "")
	util.AssertNArg(3)
}
Exemple #10
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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)
}
Exemple #11
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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)
}