func main() {
flag.Parse()
if *exclude == "" {
flag.Usage()
os.Exit(1)
}
nameSet := make(map[string]struct{})
f, err := os.Open(*exclude)
if err != nil {
log.Fatalf("failed to open exclude file %q: %v", *exclude, err)
}
ls := bufio.NewScanner(f)
for ls.Scan() {
nameSet[ls.Text()] = struct{}{}
}
err = ls.Err()
if err != nil {
log.Fatalf("failed to read exclude file: %v", err)
}
w := gff.NewWriter(os.Stdout, 60, true)
var excl *gff.Writer
if *retain {
excl = gff.NewWriter(os.Stderr, 60, true)
}
sc := featio.NewScanner(gff.NewReader(os.Stdin))
for sc.Next() {
f := sc.Feat().(*gff.Feature)
n := f.FeatAttributes.Get("Read")
if _, ok := nameSet[n]; ok {
if excl != nil {
_, err := excl.Write(f)
if err != nil {
log.Fatalf("failed to write feature: %v", err)
}
}
continue
}
_, err := w.Write(f)
if err != nil {
log.Fatalf("failed to write feature: %v", err)
}
}
if err := sc.Error(); err != nil {
log.Fatalf("error during gff read: %v", err)
}
}
func main() {
flag.Parse()
w := gff.NewWriter(os.Stdout, 60, false)
sc := featio.NewScanner(gff.NewReader(os.Stdin))
for sc.Next() {
f := sc.Feat().(*gff.Feature)
r := f.FeatAttributes.Get("Repeat")
fields := strings.Fields(r)
if len(fields) < 4 {
log.Fatal("invalid repeat attribute")
}
end, err := strconv.Atoi(fields[3])
if err != nil {
log.Fatalf("failed to parse end coordinate: %v", err)
}
remainder, err := strconv.Atoi(fields[4])
if err != nil {
log.Fatalf("failed to parse remains coordinate: %v", err)
}
length := end + remainder
if length < *thresh {
continue
}
w.Write(f)
}
if err := sc.Error(); err != nil {
log.Fatalf("error during gff read: %v", err)
}
}
// NewWriter returns a new PALS writer that write PALS alignment features to the io.Writer w.
func NewWriter(w io.Writer, prec, width int, header bool) *Writer {
gw := gff.NewWriter(w, width, header)
gw.Precision = prec
return &Writer{
w: gw,
t: &gff.Feature{Source: "pals", Feature: "hit"},
}
}
func main() {
flag.Var(&alnmat, "align", "specify the match, mismatch and gap parameters for breakpoint refinement")
flag.Parse()
if *reads == "" || (*ref == "" && *run) {
fmt.Fprintln(os.Stderr, "invalid argument: must have reads, reference and block size set")
flag.Usage()
os.Exit(1)
}
var err error
if *errFile != "" {
errStream, err = os.Create(*errFile)
if err != nil {
// Oh, the irony.
log.Fatalf("failed to create log file: %v", err)
}
defer errStream.Close()
log.SetOutput(errStream)
}
// Set up breakpoint refiner.
var br *refiner
if *refine {
refSeq, err := readContigs(*ref)
if err != nil {
log.Fatalf("failed to read reference sequences: %v", err)
}
br = &refiner{
refWindow: *refWindow,
queryWindow: *queryWindow,
minQueryGap: *minQueryGap,
minRefFlank: *minRefFlank,
ref: refSeq,
sw: makeTable(alnmat),
}
}
out := filepath.Base(*reads)
f, err := os.Create(out + ".gff")
if err != nil {
log.Fatalf("failed to create GFF outfile: %q", out+".gff")
}
w := gff.NewWriter(f, 60, true)
defer f.Close()
log.Printf("finding alignments for reads in %q", *reads)
ext := "sam"
if *useBam && !*run {
ext = "bam"
}
err = deletions(*reads, *ref, *suff, ext, *procs, *run, *window, *minSize, br, w)
if err != nil {
log.Fatalf("failed mapping: %v", err)
}
}
func main() {
names, err := checkNames(reads)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
feats, err := annotFeats(annot, classes, names)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
var rc int
for _, in := range reads {
fmt.Fprintf(os.Stderr, "Reading %q\n", in)
bf, err := boom.OpenBAM(in)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
for id := uintptr(0); ; id++ {
r, _, err := bf.Read()
if err != nil {
if err == io.EOF {
break
}
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
rc++
if r.Flags()&boom.Unmapped == 0 {
feats[r.RefID()].DoMatching(func(iv interval.IntInterface) (done bool) {
f := iv.(intGff)
if f.FeatScore == nil {
f.FeatScore = new(float64)
}
*f.FeatScore += float64(r.Len())
return
}, intBam{r, id})
}
}
bf.Close()
}
var exp gffFeatures
for _, chr := range feats {
chr.Do(func(iv interval.IntInterface) (done bool) {
f := iv.(intGff)
if f.FeatScore == nil {
return
}
*f.FeatScore /= float64(rc) * float64(f.Len())
exp = append(exp, f.Feature)
return
})
}
sort.Sort(exp)
w := gff.NewWriter(os.Stdout, 60, false)
for _, f := range exp {
w.Write(f)
}
}
func main() {
flag.Parse()
if *in == "" || *ref == "" || *mapfile == "" || *contigs == "" {
flag.Usage()
os.Exit(0)
}
refTrees, err := readAnnotations(*ref)
if err != nil {
log.Fatalf("failed to read annotation trees: %v", err)
}
mapping, err := readMappings(*mapfile)
if err != nil {
log.Fatalf("failed to read mapping file: %v", err)
}
contigLength, err := readContigs(*contigs)
if err != nil {
log.Fatalf("failed to read contig file: %v", err)
}
f, err := os.Open(*in)
if err != nil {
log.Fatalf("failed to open %q: %v", *in, err)
}
w := gff.NewWriter(os.Stdout, 60, true)
sc := featio.NewScanner(gff.NewReader(f))
for sc.Next() {
f := sc.Feat().(*gff.Feature)
ok, err := within(*buf, f.SeqName)
if err != nil {
log.Fatalf("failed to parse sequence name: %s: %v", f.SeqName, err)
}
if !ok {
log.Printf("too close to read end: excluding %+v", f)
continue
}
repeat := f.FeatAttributes.Get("Repeat")
if repeat == "" {
continue
}
fields := strings.Fields(repeat)
name := strings.Split(f.SeqName, "//")
if len(name) != 2 {
log.Fatalf("unexpected sequence name in input: %q", f.SeqName)
}
contigSide, ok := mapping[name[0]]
if !ok {
log.Fatalf("unexpected sequence name in input: %q", f.SeqName)
}
if contigSide.FeatStart+f.FeatStart < *buf {
log.Printf("too close to contig start:\n\texcluding %#v\n\tcontig %#v\n\n%d < %d", f, contigSide, contigSide.FeatStart, *buf)
continue
}
length, ok := contigLength[contigSide.SeqName]
if !ok {
log.Fatalf("unexpected sequence name in contig mapping: %q", contigSide.SeqName)
}
if length-((contigSide.FeatEnd-contigSide.FeatStart)+f.FeatEnd) < *buf {
log.Printf("too close to contig end:\n\texcluding %#v\n\tcontig %#v", f, contigSide)
continue
}
t, ok := refTrees[contigSide.SeqName]
if !ok {
log.Fatalf("no tree for %v mapped by %v", contigSide.SeqName, f.SeqName)
}
var n int
hits := t.Get(gffInterval{Feature: contigSide})
for _, h := range hits {
f := h.(gffInterval)
repeat := f.FeatAttributes.Get("Repeat")
if repeat == "" {
continue
}
hitClass := strings.Fields(repeat)[1]
if fields[1] == hitClass {
n++
}
}
if n != 0 {
log.Printf("too many hits: excluding %+v", f)
for _, h := range hits {
log.Printf("\t%+v", h.(gffInterval).Feature)
}
continue
}
w.Write(f)
}
err = sc.Error()
if err != nil {
log.Fatalf("error during GFF read: %v", err)
}
}
func main() {
flag.Parse()
if *reads == "" || *ref == "" {
fmt.Fprintln(os.Stderr, "invalid argument: must have reads, reference and block size set")
flag.Usage()
os.Exit(1)
}
var err error
if *errFile != "" {
errStream, err = os.Create(*errFile)
if err != nil {
// Oh, the irony.
log.Fatalf("failed to create log file: %v", err)
}
defer errStream.Close()
log.SetOutput(errStream)
}
if *outFile != "" {
outStream, err = os.Create(*outFile)
if err != nil {
log.Fatalf("failed to create out file: %v", err)
}
defer outStream.Close()
}
log.Printf("finding flanks of reads in %q", *reads)
core, err := hitSetFrom(*reads, *ref, *suff, *procs, *run)
if err != nil {
log.Fatalf("failed initial mapping: %v", err)
}
// Prepare flank sequences and remap them.
out := filepath.Base(*reads)
leftSeqs := out + ".left.in.fa"
rightSeqs := out + ".right.in.fa"
log.Printf("writing flanks to %q and %q", leftSeqs, rightSeqs)
err = writeFlankSeqs(*reads, core, *flank, leftSeqs, rightSeqs)
if err != nil {
log.Fatalf("failed to write flanks: %v", err)
}
log.Printf("remapping left flanks of reads from %q", leftSeqs)
left, err := hitSetFrom(leftSeqs, *ref, *suff, *procs, *run)
if err != nil {
log.Fatalf("failed left flank remapping: %v", err)
}
log.Printf("remapping right flanks of reads from %q", rightSeqs)
right, err := hitSetFrom(rightSeqs, *ref, *suff, *procs, *run)
if err != nil {
log.Fatalf("failed right flank remapping: %v", err)
}
var w *gff.Writer
if *discords {
f, err := os.Create(out + ".gff")
if err != nil {
log.Fatalf("failed to create GFF outfile: %q", out+".gff")
}
w = gff.NewWriter(f, 60, true)
defer f.Close()
}
err = writeResults(core, left, right, outStream, *length, *flank, w)
if err != nil {
log.Fatalf("failed to write results: %v", err)
}
}
func main() {
flag.Var(&alnmat, "align", "specify the match, mismatch and gap parameters")
flag.Parse()
if *in == "" {
flag.Usage()
os.Exit(1)
}
f, err := os.Open(*in)
if err != nil {
log.Fatalf("failed to open %q: %v", *in, err)
}
events := make(map[string][]*gff.Feature)
fsc := featio.NewScanner(gff.NewReader(f))
for fsc.Next() {
f := fsc.Feat().(*gff.Feature)
fields := strings.Fields(f.FeatAttributes.Get("Read"))
if len(fields) != 3 {
log.Fatalf("bad record: %+v", f)
}
events[fields[0]] = append(events[fields[0]], f)
}
if err := fsc.Error(); err != nil {
log.Fatalf("error during gff read: %v", err)
}
f.Close()
w := gff.NewWriter(os.Stdout, 60, true)
w.WriteComment("Right coordinates (field 5) and strand (field 7) are hypothetical.")
var out *os.File
if *fastaOut != "" {
out, err = os.Create(*fastaOut)
if err != nil {
log.Fatalf("failed to create fasta insertion output file %q: %v", *fastaOut, err)
}
defer out.Close()
}
hw := *window / 2
sw := makeTable(alphabet.DNAgapped, alnmat)
for _, ref := range flag.Args() {
f, err = os.Open(ref)
if err != nil {
log.Fatalf("failed to open reference %q: %v", ref, err)
}
ssc := seqio.NewScanner(fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNAgapped)))
loop:
for ssc.Next() {
seq := ssc.Seq().(*linear.Seq)
for _, f := range events[seq.Name()] {
fields := strings.Fields(f.FeatAttributes.Get("Read"))
if len(fields) != 3 {
log.Fatalf("bad record: %+v", f)
}
start, err := strconv.Atoi(fields[1])
if err != nil {
log.Fatalf("failed to get start coordinate: %v", err)
}
end, err := strconv.Atoi(fields[2])
if err != nil {
log.Fatalf("failed to get end coordinate: %v", err)
}
if out != nil {
insert := *seq
if insert.Desc != "" {
insert.Desc += " "
}
insert.Desc += fmt.Sprintf("[%d,%d)", start, end)
insert.Seq = insert.Seq[start:end]
fmt.Fprintf(out, "%60a\n", &insert)
}
var lOff, lEnd, rOff, rEnd int
// If we have refined ends, use them.
if dup := f.FeatAttributes.Get("Dup"); dup != "" {
d, err := strconv.Atoi(dup)
if err != nil {
log.Fatalf("failed to get duplication length: %v", err)
}
lOff = max(0, start-d)
lEnd = start
rOff = end
rEnd = min(len(seq.Seq), end+d)
} else {
lOff = max(0, start-hw)
lEnd = min(len(seq.Seq), start+hw)
rOff = max(0, end-hw)
rEnd = min(len(seq.Seq), end+hw)
// Ensure windows don't overlap.
if lEnd > rOff {
lEnd = (lEnd + rOff) / 2
rOff = lEnd
}
}
if lEnd-lOff < *thresh || rEnd-rOff < *thresh {
// Don't do fruitless work.
continue loop
}
left := *seq
left.ID = "prefix"
left.Seq = left.Seq[lOff:lEnd]
right := *seq
right.ID = "postfix"
right.Seq = right.Seq[rOff:rEnd]
aln, err := sw.Align(&right, &left)
if err != nil {
log.Fatal(err)
}
fa := align.Format(&right, &left, aln, '-')
for _, seg := range fa {
var n int
for _, l := range seg.(alphabet.Letters) {
if l != '-' {
n++
}
}
if n < *thresh {
continue loop
}
}
var sc int
for _, seg := range aln {
type scorer interface {
Score() int
}
sc += seg.(scorer).Score()
}
f.FeatAttributes = append(f.FeatAttributes, gff.Attribute{
Tag: "TSD", Value: fmt.Sprintf(`%v %d %d %v "%v" %d`,
fa[0], aln[len(aln)-1].Features()[0].End()+lOff,
aln[0].Features()[1].Start()+rOff, fa[1],
aln, sc),
})
w.Write(f)
}
}
if err := ssc.Error(); err != nil {
log.Fatalf("error during fasta read: %v", err)
}
f.Close()
}
}
