Beispiel #1
0
func main() {
	flag.BoolVar(&flagAllFragments, "all-fragments", flagAllFragments,
		"When set, all fragments will be shown, even if the best fragment\n"+
			"of each residue set is the same.")
	util.FlagParse(
		"fraglib align.{fasta,ali,a2m,a3m} out-csv",
		"Writes a CSV file to out-csv containing the best matching fragment\n"+
			"for each pairwise contiguous set of residues between the\n"+
			"first two proteins in the alignment.")
	util.AssertNArg(3)
	flib := util.SequenceLibrary(util.Arg(0))
	aligned := util.MSA(util.Arg(1))
	outcsv := util.CreateFile(util.Arg(2))

	csvWriter := csv.NewWriter(outcsv)
	csvWriter.Comma = '\t'
	defer csvWriter.Flush()

	pf := func(record ...string) {
		util.Assert(csvWriter.Write(record), "Problem writing to '%s'", outcsv)
	}
	pf("start1", "end1", "start2", "end2", "frag1", "frag2", "rat1", "rat2")
	iter := newContiguous(
		flib.FragmentSize(), aligned.GetFasta(0), aligned.GetFasta(1))
	for iter.next() {
		best1 := flib.BestSequenceFragment(iter.res1)
		best2 := flib.BestSequenceFragment(iter.res2)
		if !flagAllFragments && best1 == best2 {
			continue
		}
		if best1 == -1 || best2 == -1 {
			continue
		}
		p1 := flib.AlignmentProb(best1, iter.res1)
		p2 := flib.AlignmentProb(best2, iter.res2)
		if p1.Distance(p2) > 0.14 {
			continue
		}
		pf(
			fmt.Sprintf("%d", iter.s1()),
			fmt.Sprintf("%d", iter.e1()),
			fmt.Sprintf("%d", iter.s2()),
			fmt.Sprintf("%d", iter.e2()),
			fmt.Sprintf("%d", best1),
			fmt.Sprintf("%d", best2),
			fmt.Sprintf("%f", p1),
			fmt.Sprintf("%f", p2),
		)
	}
}
Beispiel #2
0
func main() {
	flag.BoolVar(&flagAllFragments, "all-fragments", flagAllFragments,
		"When set, all fragments will be shown, even if the best fragment\n"+
			"of each ATOM set is the same.")
	util.FlagParse(
		"fraglib align.{fasta,ali,a2m,a3m} pdb-file out-csv",
		"Writes a CSV file to out-csv containing the best matching fragment\n"+
			"for each pairwise contiguous set of alpha-carbon atoms of the\n"+
			"first two proteins in the alignment and PDB file.")
	util.AssertNArg(4)
	flib := util.StructureLibrary(util.Arg(0))
	aligned := util.MSA(util.Arg(1))
	pentry := util.PDBRead(util.Arg(2))
	outcsv := util.CreateFile(util.Arg(3))

	csvWriter := csv.NewWriter(outcsv)
	csvWriter.Comma = '\t'
	defer csvWriter.Flush()

	pf := func(record ...string) {
		util.Assert(csvWriter.Write(record), "Problem writing to '%s'", outcsv)
	}
	pf("start1", "end1", "start2", "end2", "frag1", "frag2", "frag_rmsd")
	iter := newContiguous(
		flib.FragmentSize(),
		aligned.GetFasta(0), aligned.GetFasta(1),
		pentry.Chains[0], pentry.Chains[1])
	for iter.next() {
		best1 := flib.BestStructureFragment(iter.atoms1)
		best2 := flib.BestStructureFragment(iter.atoms2)
		if !flagAllFragments && best1 == best2 {
			continue
		}
		bestRmsd := structure.RMSD(flib.Atoms(best1), flib.Atoms(best2))
		pf(
			fmt.Sprintf("%d", iter.s1()),
			fmt.Sprintf("%d", iter.e1()),
			fmt.Sprintf("%d", iter.s2()),
			fmt.Sprintf("%d", iter.e2()),
			fmt.Sprintf("%d", best1),
			fmt.Sprintf("%d", best2),
			fmt.Sprintf("%f", bestRmsd),
		)
	}
}