func viewLib(c *command) {
c.assertNArg(1)
lib := util.Library(c.flags.Arg(0))
fmt.Printf("Name: %s\n", lib.Name())
fmt.Printf("Tag: %s\n", strings.Join(libraryTag(lib), "/"))
fmt.Printf("Size: %d\n", lib.Size())
fmt.Printf("Fragment Size: %d\n", lib.FragmentSize())
fmt.Printf("IsStructure: %v\n", fragbag.IsStructure(lib))
fmt.Printf("IsSequence: %v\n", fragbag.IsSequence(lib))
}
func mkPaired(c *command) {
c.assertNArg(2)
in := util.Library(c.flags.Arg(0))
outPath := c.flags.Arg(1)
util.AssertOverwritable(outPath, flagOverwrite)
if _, ok := in.(fragbag.WeightedLibrary); ok {
util.Fatalf("%s is a weighted library (not allowed)", in.Name())
}
name := fmt.Sprintf("paired-%s", in.Name())
if fragbag.IsStructure(in) {
var pairs [][]structure.Coords
lib := in.(fragbag.StructureLibrary)
nfrags := lib.Size()
for i := 0; i < nfrags; i++ {
for j := 0; j < nfrags; j++ {
if i == j {
continue
}
f1, f2 := lib.Atoms(i), lib.Atoms(j)
pairs = append(pairs, append(f1, f2...))
}
}
pairLib, err := fragbag.NewStructureAtoms(name, pairs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), pairLib)
} else if strings.Contains(in.Tag(), "hmm") {
var pairs []*seq.HMM
lib := in.(fragbag.SequenceLibrary)
nfrags := lib.Size()
for i := 0; i < nfrags; i++ {
for j := 0; j < nfrags; j++ {
if i == j {
continue
}
f1, f2 := lib.Fragment(i).(*seq.HMM), lib.Fragment(j).(*seq.HMM)
pairs = append(pairs, seq.HMMCat(f1, f2))
}
}
pairLib, err := fragbag.NewSequenceHMM(name, pairs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), pairLib)
} else if strings.Contains(in.Tag(), "profile") {
util.Fatalf("Sequence profiles not implemented.")
} else {
util.Fatalf("Unrecognized fragment library: %s", in.Tag())
}
}
func mkBowDb(c *command) {
c.assertLeastNArg(3)
dbPath := c.flags.Arg(0)
flib := util.Library(c.flags.Arg(1))
bowPaths := c.flags.Args()[2:]
util.AssertOverwritable(dbPath, flagOverwrite)
db, err := bowdb.Create(flib, dbPath)
util.Assert(err)
bows := util.ProcessBowers(bowPaths, flib, false, flagCpu, util.FlagQuiet)
for b := range bows {
db.Add(b)
}
util.Assert(db.Close())
}
func vectors(c *command) {
c.assertLeastNArg(2)
flib := util.Library(c.flags.Arg(0))
bowPaths := c.flags.Args()[1:]
tostrs := func(freqs []float32) []string {
strs := make([]string, len(freqs))
for i := range freqs {
strs[i] = strconv.FormatFloat(float64(freqs[i]), 'f', -1, 32)
}
return strs
}
results := util.ProcessBowers(bowPaths, flib, flagPairdistModels,
flagCpu, true)
for r := range results {
fmt.Printf("%s\t%s\n", r.Id, strings.Join(tostrs(r.Bow.Freqs), "\t"))
}
}
func pairdist(c *command) {
c.assertLeastNArg(2)
flib := util.Library(c.flags.Arg(0))
bowPaths := c.flags.Args()[1:]
bows := make([]bow.Bowed, 0, 1000)
results := util.ProcessBowers(bowPaths, flib, flagPairdistModels,
flagCpu, util.FlagQuiet)
for r := range results {
bows = append(bows, r)
}
for i := 0; i < len(bows); i++ {
b1 := bows[i]
for j := i + 1; j < len(bows); j++ {
b2 := bows[j]
dist := math.Abs(b1.Bow.Cosine(b2.Bow))
fmt.Printf("%s\t%s\t%0.4f\n", b1.Id, b2.Id, dist)
}
}
}