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),
)
}
}
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),
)
}
}