// WriteMetaData writes a meta data line to a GFF file. The type of metadata line
// depends on the type of d: strings and byte slices are written verbatim, an int is
// interpreted as a version number and can only be written before any other data,
// feat.Moltype and gff.Sequence types are written as sequence type lines, gff.Features
// and gff.Regions are written as sequence regions, sequences are written _n GFF
// format and time.Time values are written as date line. All other type return an
// ErrNotHandled.
func (w *Writer) WriteMetaData(d interface{}) (n int, err error) {
defer func() { w.header = true }()
switch d := d.(type) {
case string:
return fmt.Fprintf(w.w, "##%s\n", d)
case []byte:
return fmt.Fprintf(w.w, "##%s\n", d)
case int:
if w.header {
return 0, ErrCannotHeader
}
return fmt.Fprintf(w.w, "##gff-version %d\n", d)
case feat.Moltype:
return fmt.Fprintf(w.w, "##Type %s\n", d)
case Sequence:
return fmt.Fprintf(w.w, "##Type %s %s\n", d.Type, d.SeqName)
case *Feature:
return fmt.Fprintf(w.w, "##sequence-region %s %d %d\n", d.SeqName, feat.ZeroToOne(d.FeatStart), d.FeatEnd)
case feat.Feature:
return w.Write(d)
case time.Time:
return fmt.Fprintf(w.w, "##date %s\n", d.Format(w.TimeFormat))
}
return 0, ErrNotHandled
}
// Write writes a single feature and return the number of bytes written and any error.
func (w *Writer) Write(pair *Pair) (n int, err error) {
t := w.t
t.SeqName = pair.B.Location().Name()
t.FeatStart = pair.B.Start()
t.FeatEnd = pair.B.End()
t.FeatScore = floatPtr(float64(pair.Score))
t.FeatStrand = pair.Strand
t.FeatFrame = gff.NoFrame
t.FeatAttributes = append(t.FeatAttributes[:0],
gff.Attribute{
Tag: "Target",
Value: fmt.Sprintf("%s %d %d", pair.A.Location().Name(), feat.ZeroToOne(pair.A.Start()), pair.A.End()),
},
gff.Attribute{
Tag: "maxe",
Value: fmt.Sprintf("%.2g", pair.Error),
},
)
return w.w.Write(t)
}
// Write writes a single feature and return the number of bytes written and any error.
// gff.Features are written as a canonical GFF line, seq.Sequences are written as inline
// sequence in GFF format (note that only sequences of feat.Moltype DNA, RNA and Protein
// are supported). gff.Sequences are not handled as they have a zero length. All other
// feat.Feature are written as sequence region metadata lines.
func (w *Writer) Write(f feat.Feature) (n int, err error) {
if f.Start() >= f.End() {
return 0, ErrBadFeature
}
w.header = true
switch f := f.(type) {
case *Feature:
defer func() {
if err != nil {
return
}
_, err = w.w.Write([]byte{'\n'})
if err != nil {
return
}
n++
}()
n, err = fmt.Fprintf(w.w, "%s\t%s\t%s\t%d\t%d\t",
f.SeqName,
f.Source,
f.Feature,
feat.ZeroToOne(f.FeatStart),
f.FeatEnd,
)
if err != nil {
return n, err
}
var _n int
if f.FeatScore != nil && !math.IsNaN(*f.FeatScore) {
if w.Precision < 0 {
_n, err = fmt.Fprintf(w.w, "%v", *f.FeatScore)
} else {
_n, err = fmt.Fprintf(w.w, "%.*f", w.Precision, *f.FeatScore)
}
if err != nil {
return n, err
}
n += _n
} else {
_, err = w.w.Write([]byte{'.'})
if err != nil {
return n, err
}
n++
}
_n, err = fmt.Fprintf(w.w, "\t%s\t%s",
f.FeatStrand,
f.FeatFrame,
)
n += _n
if err != nil {
return n, err
}
if f.FeatAttributes != nil {
_n, err = fmt.Fprintf(w.w, "\t%v", f.FeatAttributes)
if err != nil {
return n, err
}
n += _n
} else if f.Comments != "" {
_, err = w.w.Write([]byte{'\t'})
if err != nil {
return
}
n++
}
if f.Comments != "" {
_n, err = fmt.Fprintf(w.w, "\t%s", f.Comments)
n += _n
}
return n, err
case seq.Sequence:
sw := fasta.NewWriter(w.w, w.Width)
moltype := f.Alphabet().Moltype()
if moltype < feat.DNA || moltype > feat.Protein {
return 0, ErrNotHandled
}
sw.IDPrefix = [...][]byte{
feat.DNA: []byte("##DNA "),
feat.RNA: []byte("##RNA "),
feat.Protein: []byte("##Protein "),
}[moltype]
sw.SeqPrefix = []byte("##")
n, err = sw.Write(f)
if err != nil {
return n, err
}
var _n int
_n, err = w.w.Write([...][]byte{
feat.DNA: []byte("##end-DNA\n"),
feat.RNA: []byte("##end-RNA\n"),
feat.Protein: []byte("##end-Protein\n"),
}[moltype])
return n + _n, err
case Sequence:
return 0, ErrNotHandled
case *Region:
return fmt.Fprintf(w.w, "##sequence-region %s %d %d\n", f.SeqName, feat.ZeroToOne(f.RegionStart), f.RegionEnd)
default:
return fmt.Fprintf(w.w, "##sequence-region %s %d %d\n", f.Name(), feat.ZeroToOne(f.Start()), f.End())
}
}
// deletions analyses *sam.Records from mapping reads to the given reference
// using the suffix array file if provided. If run is false, blasr is not
// run and the existing blasr output is used to provide the *sam.Records.
// procs specifies the number of blasr threads to use.
func deletions(reads, ref, suff, ext string, procs int, run bool, window, min int, br *refiner, w *gff.Writer) error {
base := filepath.Base(reads)
b := blasr.BLASR{
Cmd: *blasrPath,
Reads: reads, Genome: ref, SuffixArray: suff,
BestN: 1,
SAM: true,
Clipping: "soft",
SAMQV: true,
CIGARSeqMatch: true,
Aligned: base + ".blasr." + ext,
Unaligned: base + ".blasr.unmapped.fasta",
Procs: procs,
}
if run {
cmd, err := b.BuildCommand()
if err != nil {
return err
}
cmd.Stdout = errStream
cmd.Stderr = errStream
err = cmd.Run()
if err != nil {
return err
}
}
f, err := os.Open(b.Aligned)
if err != nil {
return err
}
defer f.Close()
cost := [...]float64{
sam.CigarInsertion: -2,
sam.CigarDeletion: -2,
sam.CigarEqual: 1,
sam.CigarMismatch: -1,
// Included for explicitness
sam.CigarSoftClipped: 0,
// Included to ensure no bounds panic.
// All CIGAR operations not listed above
// are given a zero cost.
sam.CigarBack: 0,
}
_, err = w.WriteComment(fmt.Sprintf("smoothing window=%d", window))
if err != nil {
return nil
}
_, err = w.WriteComment(fmt.Sprintf("minimum feature length=%d", min))
if err != nil {
return nil
}
gf := &gff.Feature{
Source: "reefer",
Feature: "discordance",
FeatFrame: gff.NoFrame,
FeatAttributes: gff.Attributes{{Tag: "Read"}, {Tag: "Dup"}},
}
var sr interface {
Read() (*sam.Record, error)
}
switch ext {
case "sam":
sr, err = sam.NewReader(f)
if err != nil {
return err
}
case "bam":
var br *bam.Reader
br, err = bam.NewReader(f, 0)
if err != nil {
return err
}
defer br.Close()
sr = br
default:
panic("reefer: invalid extension")
}
for {
r, err := sr.Read()
if err != nil {
if err != io.EOF {
return err
}
break
}
var (
scores []costPos
ref = r.Start()
query int
)
for _, co := range r.Cigar {
for i := 0; i < co.Len(); i++ {
scores = append(scores, costPos{
ref: ref,
query: query,
cost: cost[co.Type()],
})
consume := co.Type().Consumes()
ref += consume.Reference
query += consume.Query
}
}
if len(scores) <= window {
continue
}
smoothed := make([]costPos, len(scores)-window)
for i := range scores[:len(scores)-window] {
smoothed[i] = mean(scores[i : i+window])
}
var d deletion
for i, v := range smoothed[1:] {
switch {
case d.record == nil && v.cost < 0 && smoothed[i].cost >= 0:
d = deletion{record: r, rstart: v.ref + 1, qstart: v.query + 1}
case d.record != nil && v.cost >= 0 && smoothed[i].cost < 0:
d.rend = v.ref
d.qend = v.query
if d.rend-d.rstart >= min || d.qend-d.qstart >= min {
gf.SeqName = d.record.Ref.Name()
gf.FeatStrand = strandFor(d.record)
if gf.FeatStrand == seq.Minus {
len := d.record.Seq.Length
d.qstart, d.qend = len-d.qend, len-d.qstart
}
// Adjust ends based on paired SW alignments.
var refined bool
d, refined, err = br.adjust(d)
if err != nil && *verbose {
log.Printf("failed alignment %s: %v", d.record.Name, err)
}
gf.FeatStart = d.rstart
gf.FeatEnd = d.rend
if gf.FeatStart == gf.FeatEnd {
// This is disgusting garbage resulting from
// GFF not allowing zero length features.
gf.FeatEnd++
}
if refined {
gf.FeatAttributes = gf.FeatAttributes[:2]
gf.FeatAttributes[1].Value = strconv.Itoa(d.dup)
} else {
gf.FeatAttributes = gf.FeatAttributes[:1]
}
gf.FeatAttributes[0].Value = fmt.Sprintf("%s %d %d", d.record.Name, feat.ZeroToOne(d.qstart), d.qend)
_, err = w.Write(gf)
if err != nil {
return err
}
}
d.record = nil
}
}
}
return nil
}