Beispiel #1
0
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))
}
Beispiel #2
0
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())
	}
}
Beispiel #3
0
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())
}
Beispiel #4
0
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"))
	}
}
Beispiel #5
0
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)
		}
	}
}