Ejemplo n.º 1
0
func init() {
	flag.StringVar(&flagChain, "chain", flagChain,
		"When set, only this chain will be tested for a correspondence. "+
			"Otherwise, all chains will be tested.")

	util.FlagParse("pdb-file", "")
	util.AssertNArg(1)
}
Ejemplo n.º 2
0
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)
}
Ejemplo n.º 3
0
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)
}
Ejemplo n.º 4
0
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())
}
Ejemplo n.º 5
0
func init() {
	flag.BoolVar(&flagPaths, "paths", flagPaths,
		"When set, the full path of each PDB chain identifier will be\n"+
			"displayed, based on the value of the PDB_PATH environment\n"+
			"variable.")

	util.FlagParse("pdb-select-file",
		"Given a file in the PDB Select format, output a list of PDB chain "+
			"identifiers (one per line).")
	util.AssertNArg(1)
}
Ejemplo n.º 6
0
func init() {
	flag.StringVar(&flagChain, "chain", flagChain,
		"This may be set to one or more chain identifiers. Only amino acids "+
			"belonging to a chain specified will be included.")
	flag.StringVar(&flagSplit, "split", flagSplit,
		"When set, each FASTA entry produced will be written to a file in the "+
			"specified directory with the PDB id code and chain identifier as "+
			"the name.")

	util.FlagParse("in-pdb-file [out-fasta-file]", "")

	if util.NArg() != 1 && util.NArg() != 2 {
		util.Usage()
	}
}
Ejemplo n.º 7
0
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)
	}
}
Ejemplo n.º 8
0
func init() {
	util.FlagParse("fasta-file",
		"Quickly count the number of sequences in a fasta file.")
	util.AssertNArg(1)
}
Ejemplo n.º 9
0
func init() {
	util.FlagParse("fmap-file", "")
	util.AssertNArg(1)
}
Ejemplo n.º 10
0
func init() {
	util.FlagParse("hhm-file start end", "")
	util.AssertNArg(3)
}
Ejemplo n.º 11
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)
}
Ejemplo n.º 12
0
func init() {
	util.FlagUse("cpu")
	util.FlagParse("frag-lib-dir fmap-file out-bow", "")
	util.AssertNArg(3)
}
Ejemplo n.º 13
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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)
}
Ejemplo n.º 14
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func init() {
	util.FlagParse("bow1 bow2", "")
	util.AssertNArg(2)
}
Ejemplo n.º 15
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func init() {
	util.FlagParse("fasta-file out-dir",
		"Split a single FASTA file into a set of files for each sequence.")
	util.AssertNArg(2)
}
Ejemplo n.º 16
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func init() {
	u := "pdb-file chain-id start stop pdb-file chain-id start stop"
	util.FlagParse(u, "")
	util.AssertNArg(8)
}
Ejemplo n.º 17
0
func init() {
	u := "fraglib pdb-file [ chain-id [ start stop ] ]"
	util.FlagParse(u, "")
	util.AssertLeastNArg(2)
}