Example #1
0
func mkStructure(c *command) {
	c.assertNArg(2)

	brkFile := c.flags.Arg(0)
	saveto := c.flags.Arg(1)

	util.AssertOverwritable(saveto, flagOverwrite)

	brkContents, err := ioutil.ReadAll(util.OpenFile(c.flags.Arg(0)))
	util.Assert(err)

	pdbFragments := bytes.Split(brkContents, []byte("TER"))
	fragments := make([][]structure.Coords, 0)
	for i, pdbFrag := range pdbFragments {
		pdbFrag = bytes.TrimSpace(pdbFrag)
		if len(pdbFrag) == 0 {
			continue
		}
		fragments = append(fragments, coords(i, pdbFrag))
	}

	libName := stripExt(path.Base(brkFile))
	lib, err := fragbag.NewStructureAtoms(libName, fragments)
	util.Assert(err)
	fragbag.Save(util.CreateFile(saveto), lib)
}
Example #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())
	}
}