func ExampleFitted_Align() {
fsa := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("GTTGACAGACTAGATTCACG"))}
fsa.Alpha = alphabet.DNAgapped
fsb := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("GACAGACGA"))}
fsb.Alpha = alphabet.DNAgapped
// Query letter
// - A C G T
// - 0 -5 -5 -5 -5
// A -5 10 -3 -1 -4
// C -5 -3 9 -5 0
// G -5 -1 -5 7 -3
// T -5 -4 0 -3 8
fitted := Fitted{
{0, -5, -5, -5, -5},
{-5, 10, -3, -1, -4},
{-5, -3, 9, -5, 0},
{-5, -1, -5, 7, -3},
{-5, -4, 0, -3, 8},
}
aln, err := fitted.Align(fsa, fsb)
if err == nil {
fmt.Printf("%s\n", aln)
fa := Format(fsa, fsb, aln, '-')
fmt.Printf("%s\n%s\n", fa[0], fa[1])
}
// Output:
// [[3,10)/[0,7)=62 [10,12)/-=-10 [12,14)/[7,9)=17]
// GACAGACTAGA
// GACAGAC--GA
}
func ExampleSW_Align_2() {
swsa := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("AAAATTTAAAA"))}
swsa.Alpha = alphabet.DNAgapped
swsb := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("AAAAGGGAAAA"))}
swsb.Alpha = alphabet.DNAgapped
// w(gap) = 0
// w(match) = +2
// w(mismatch) = -1
smith := SW{
{0, 0, 0, 0, 0},
{0, 2, -1, -1, -1},
{0, -1, 2, -1, -1},
{0, -1, -1, 2, -1},
{0, -1, -1, -1, 2},
}
aln, err := smith.Align(swsa, swsb)
if err == nil {
fmt.Printf("%v\n", aln)
fa := Format(swsa, swsb, aln, '-')
fmt.Printf("%s\n%s\n", fa[0], fa[1])
}
// Output:
// [[0,4)/[0,4)=8 -/[4,7)=0 [4,7)/-=0 [7,11)/[7,11)=8]
// AAAA---TTTAAAA
// AAAAGGG---AAAA
}
func ExampleNW_Align() {
nwsa := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("AGACTAGTTA"))}
nwsa.Alpha = alphabet.DNAgapped
nwsb := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("GACAGACG"))}
nwsb.Alpha = alphabet.DNAgapped
// Query letter
// - A C G T
// - 0 -5 -5 -5 -5
// A -5 10 -3 -1 -4
// C -5 -3 9 -5 0
// G -5 -1 -5 7 -3
// T -5 -4 0 -3 8
needle := NW{
{0, -5, -5, -5, -5},
{-5, 10, -3, -1, -4},
{-5, -3, 9, -5, 0},
{-5, -1, -5, 7, -3},
{-5, -4, 0, -3, 8},
}
aln, err := needle.Align(nwsa, nwsb)
if err == nil {
fmt.Printf("%s\n", aln)
fa := Format(nwsa, nwsb, aln, '-')
fmt.Printf("%s\n%s\n", fa[0], fa[1])
}
// Output:
//[[0,1)/-=-5 [1,4)/[0,3)=26 [4,5)/-=-5 [5,10)/[3,8)=12]
// AGACTAGTTA
// -GAC-AGACG
}
func ExampleSW_Align_1() {
swsa := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("ACACACTA"))}
swsa.Alpha = alphabet.DNAgapped
swsb := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("AGCACACA"))}
swsb.Alpha = alphabet.DNAgapped
// w(gap) = -1
// w(match) = +2
// w(mismatch) = -1
smith := SW{
{0, -1, -1, -1, -1},
{-1, 2, -1, -1, -1},
{-1, -1, 2, -1, -1},
{-1, -1, -1, 2, -1},
{-1, -1, -1, -1, 2},
}
aln, err := smith.Align(swsa, swsb)
if err == nil {
fmt.Printf("%v\n", aln)
fa := Format(swsa, swsb, aln, '-')
fmt.Printf("%s\n%s\n", fa[0], fa[1])
}
// Output:
// [[0,1)/[0,1)=2 -/[1,2)=-1 [1,6)/[2,7)=10 [6,7)/-=-1 [7,8)/[7,8)=2]
// A-CACACTA
// AGCACAC-A
}
// Read a single sequence and return it and potentially an error. Note that
// a non-nil returned error may be associated with a valid sequence, so it is
// the responsibility of the caller to examine the error to determine whether
// the read was successful.
// Note that if the Reader's template type returns different non-nil error
// values from calls to SetName and SetDescription, a new error string will be
// returned on each call to Read. So to allow direct error comparison these
// methods should return the same error.
func (r *Reader) Read() (seq.Sequence, error) {
var (
buff, line []byte
isPrefix bool
s seq.Sequence
)
defer func() {
if r.working == nil {
r.err = nil
}
}()
for {
var err error
if buff, isPrefix, err = r.r.ReadLine(); err != nil {
if err != io.EOF || r.working == nil {
return nil, err
}
s, err = r.working, r.err
r.working = nil
return s, err
}
line = append(line, buff...)
if isPrefix {
continue
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
if bytes.HasPrefix(line, r.IDPrefix) {
if r.working == nil {
r.working, r.err = r.header(line)
line = nil
} else {
s, err = r.working, r.err
r.working, r.err = r.header(line)
return s, err
}
} else if bytes.HasPrefix(line, r.SeqPrefix) {
if r.working == nil {
return nil, fmt.Errorf("fasta: badly formed line %q", line)
}
line = bytes.Join(bytes.Fields(line[len(r.SeqPrefix):]), nil)
r.working.AppendLetters(alphabet.BytesToLetters(line)...)
line = nil
} else {
return nil, fmt.Errorf("fasta: badly formed line %q", line)
}
}
}
func ExampleFittedAffine_Align() {
fsa := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("ATTGGCAATGA"))}
fsa.Alpha = alphabet.DNAgapped
fsb := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("ATAGGAA"))}
fsb.Alpha = alphabet.DNAgapped
// Query letter
// - A C G T
// - 0 -1 -1 -1 -1
// A -1 1 -1 -1 -1
// C -1 -1 1 -1 -1
// G -1 -1 -1 1 -1
// T -1 -1 -1 -1 1
//
// Gap open: -5
fitted := FittedAffine{
Matrix: Linear{
{0, -1, -1, -1, -1},
{-1, 1, -1, -1, -1},
{-1, -1, 1, -1, -1},
{-1, -1, -1, 1, -1},
{-1, -1, -1, -1, 1},
},
GapOpen: -5,
}
aln, err := fitted.Align(fsa, fsb)
if err == nil {
fmt.Printf("%s\n", aln)
fa := Format(fsa, fsb, aln, '-')
fmt.Printf("%s\n%s\n", fa[0], fa[1])
}
// Output:
// [[0,7)/[0,7)=3]
// ATTGGCA
// ATAGGAA
}
func ExampleNWAffine_Align() {
nwsa := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("ATAGGAAG"))}
nwsa.Alpha = alphabet.DNAgapped
nwsb := &linear.Seq{Seq: alphabet.BytesToLetters([]byte("ATTGGCAATG"))}
nwsb.Alpha = alphabet.DNAgapped
// Query letter
// - A C G T
// - 0 -1 -1 -1 -1
// A -1 1 -1 -1 -1
// C -1 -1 1 -1 -1
// G -1 -1 -1 1 -1
// T -1 -1 -1 -1 1
//
// Gap open: -5
needle := NWAffine{
Matrix: Linear{
{0, -1, -1, -1, -1},
{-1, 1, -1, -1, -1},
{-1, -1, 1, -1, -1},
{-1, -1, -1, 1, -1},
{-1, -1, -1, -1, 1},
},
GapOpen: -5,
}
aln, err := needle.Align(nwsa, nwsb)
if err == nil {
fmt.Printf("%s\n", aln)
fa := Format(nwsa, nwsb, aln, '-')
fmt.Printf("%s\n%s\n", fa[0], fa[1])
}
// Output:
// [[0,7)/[0,7)=3 -/[7,9)=-7 [7,8)/[9,10)=1]
// ATAGGAA--G
// ATTGGCAATG
}
func (r *Reader) metaSeq(moltype, id []byte) (seq.Sequence, error) {
var line, body []byte
var err error
for {
line, err = r.r.ReadBytes('\n')
if err != nil {
if err == io.EOF {
return nil, err
}
return nil, &csv.ParseError{Line: r.line, Err: err}
}
r.line++
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
if len(line) < 2 || !bytes.HasPrefix(line, []byte("##")) {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadSequence}
}
line = bytes.TrimSpace(line[2:])
if unsafeString(line) == "end-"+unsafeString(moltype) {
break
} else {
line = bytes.Join(bytes.Fields(line), nil)
body = append(body, line...)
}
}
var alpha alphabet.Alphabet
switch feat.ParseMoltype(unsafeString(moltype)) {
case feat.DNA:
alpha = alphabet.DNA
case feat.RNA:
alpha = alphabet.RNA
case feat.Protein:
alpha = alphabet.Protein
default:
return nil, ErrBadMoltype
}
s := linear.NewSeq(string(id), alphabet.BytesToLetters(body), alpha)
return s, err
}
// Helper
func stringToSeq(s string) *linear.Seq {
return linear.NewSeq("", alphabet.BytesToLetters([]byte(s)), alphabet.DNA)
}
func main() {
if len(os.Args) < 2 {
fmt.Fprintln(os.Stderr, "invalid invocation: must have at least one reads file")
os.Exit(1)
}
extract := make(map[string][2]int)
sc := featio.NewScanner(gff.NewReader(os.Stdin))
for sc.Next() {
f := sc.Feat().(*gff.Feature)
read := f.FeatAttributes.Get("Read")
if read == "" {
continue
}
fields := strings.Fields(read)
name := fields[0]
start, err := strconv.Atoi(fields[1])
if err != nil {
log.Fatalf("failed to parse %q: %v", read, err)
}
end, err := strconv.Atoi(fields[2])
if err != nil {
log.Fatalf("failed to parse %q: %v", read, err)
}
extract[name] = [2]int{start, end}
}
err := sc.Error()
if err != nil {
log.Fatalf("error during GFF read: %v", err)
}
for _, reads := range os.Args[1:] {
sf, err := os.Open(reads)
if err != nil {
log.Fatalf("failed to open %q: %v", reads, err)
}
sr, err := sam.NewReader(sf)
if err != nil {
log.Fatalf("failed to open SAM input %q: %v", reads, err)
}
for {
r, err := sr.Read()
if err != nil {
if err != io.EOF {
log.Fatalf("unexpected error reading SAM: %v", err)
}
break
}
v, ok := extract[r.Name]
if !ok {
continue
}
// Currently reefer only expects a single hit per read,
// so any multiples are due to duplicate read file input.
// Update this behaviour if we change reefer to look at
// remapping soft-clipped segments.
delete(extract, r.Name)
reverse := r.Flags&sam.Reverse != 0
rng := fmt.Sprintf("//%d_%d", v[0], v[1])
if reverse {
rng += "(-)"
len := r.Seq.Length
v[0], v[1] = len-v[1], len-v[0]
}
v[0] = feat.OneToZero(v[0])
s := linear.NewSeq(
r.Name+rng,
alphabet.BytesToLetters(r.Seq.Expand())[v[0]:v[1]],
alphabet.DNA,
)
if reverse {
s.Desc = "(sequence revcomp relative to read)"
}
fmt.Printf("%60a\n", s)
}
sf.Close()
}
}
// adjustDeletion performs a deletion ends refinement based on a
// pair of Smith-Waterman alignments.
//
// l s e r
// ref: -----|------+~~~+------|----------
//
// query_left: ----|-----------+~~~~~~|~~~~~~+---------------
// l s m e
// query_right: ----------------+~~~~~~|~~~~~~+-----------|---
// s m e r
//
// where ~~ is the region found by CIGAR score walking above in the
// deletions function.
//
// align ref(l..r) with query_left(l..m) -> ref(s)-query_left(s)
// align ref(l..r) with query_right(m..r) -> ref(e)-query_left(e)
//
// This can give either of two outcomes:
// 1. ref(s) < ref(e)
// 2. ref(e) <= ref(s)
//
// The first case is a standard colinear alignment:
//
// s e
// ref: -----------+---+-----------------
// / \
// / \
// / \
// / \
// query: ----------------+-------------+---------------
// s e
//
//
// The second case is a non-colinear alignment:
//
// e s
// ref: -----------+---+-----------------
// \ /
// /
// / \
// / \
// / \
// / \
// / \
// / \
// query: ----------------+-------------+---------------
// s e
//
//
// which has a potential target site duplication interpretation:
//
// e s
// ref: -----------+---+-----------------
// / \ / \
// / / \
// / / \ \
// / / \ \
// / / \ \
// / / \ \
// / / \ \
// / / \ \
// query: ------------+---+-------------+---+-----------
// s e
//
// adjustDeletions handles the second case by making ref(s=e) for the
// reference and adding annotation for the length of the duplication
// (d) in ref:
//
// s|e s+d
// ref: -----------+---+-----------------
// / \ / \
// / / \
// / / \ \
// / / \ \
// / / \ \
// / / \ \
// / / \ \
// / / \ \
// query: ------------+---+-------------+---+-----------
// s-d s e e+d
//
func (r *refiner) adjust(d deletion) (refined deletion, ok bool, err error) {
if r == nil {
return d, false, nil
}
if d.qend-d.qstart < d.rend-d.rstart {
// Do not do any work for deletions.
return d, false, fmt.Errorf("not an insertion: len(q)=%d len(r)=%d", d.qend-d.qstart, d.rend-d.rstart)
}
name := d.record.Ref.Name()
ref, ok := r.ref[name]
if !ok {
return d, false, fmt.Errorf("no reference sequence for %q", name)
}
rs := *ref
rOff := max(0, d.rstart-r.refWindow/2)
rs.Seq = ref.Seq[rOff:min(d.rend+r.refWindow/2, len(ref.Seq))]
q := alphabet.BytesToLetters(d.record.Seq.Expand())
// Align the left junction of the qeuery to
// the reference around the indel site.
qsl := linear.NewSeq(d.record.Name, nil, alphabet.DNAgapped)
qOffLeft := max(0, d.qstart-r.queryWindow)
qsl.Seq = q[qOffLeft : (d.qstart+d.qend)/2]
alnl, err := r.sw.Align(&rs, qsl)
if err != nil {
return d, false, err
}
// Align the right junction of the qeuery to
// the reference around the indel site.
qsr := linear.NewSeq(d.record.Name, nil, alphabet.DNAgapped)
qOffRight := (d.qstart + d.qend) / 2
qsr.Seq = q[qOffRight:min(d.qend+r.queryWindow, len(q))]
alnr, err := r.sw.Align(&rs, qsr)
if err != nil {
return d, false, err
}
// Get left and right ends of insertion in read
// and the aligned segment of the reference.
left := alnl[len(alnl)-1].Features()
right := alnr[0].Features()
// Bail out if the alignment extends too far.
// We might have continued alignment.
if flank := right[0].Start(); flank < r.minRefFlank {
return d, false, fmt.Errorf("skipping: right ref flank less than %d from left: len(flank)=%v",
r.minRefFlank, flank)
}
if flank := left[0].End(); len(rs.Seq)-flank < r.minRefFlank {
return d, false, fmt.Errorf("skipping: left ref flank less than %d from right: len(flank)=%v",
r.minRefFlank, len(rs.Seq)-flank)
}
centrel := r.queryWindow + (d.qend-d.qstart)/2
centrer := 0
// Bail out if the insertion is too short.
// We might have continued alignment.
if gap := centrel - left[1].End(); gap < r.minQueryGap {
return d, false, fmt.Errorf("skipping left: left query gap less than %d from centre: len(gap)=%v",
r.minQueryGap, gap)
}
if gap := right[1].Start() - centrer; gap < r.minQueryGap {
return d, false, fmt.Errorf("skipping right: right query gap less than %d from centre: len(gap)=%v",
r.minQueryGap, gap)
}
d.rstart = rOff + left[0].End()
d.rend = rOff + right[0].Start()
if d.rend <= d.rstart {
d.dup = d.rstart - d.rend
d.rstart = d.rend
}
d.qstart = qOffLeft + left[1].End()
d.qend = qOffRight + alnr[0].Features()[1].Start()
return d, true, nil
}
##DNA <seqname>
##acggctcggattggcgctggatgatagatcagacgac
##...
##end-DNA
##RNA <seqname>
##acggcucggauuggcgcuggaugauagaucagacgac
##...
##end-RNA
##Protein <seqname>
##MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF
##...
##end-Protein
##sequence-region <seqname> 1 5
`,
feat: []feat.Feature{
linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggctcggattggcgctggatgatagatcagacgac...")), alphabet.DNA),
linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggcucggauuggcgcuggaugauagaucagacgac...")), alphabet.RNA),
linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF...")), alphabet.Protein),
&Region{Sequence: Sequence{SeqName: "<seqname>", Type: feat.DNA}, RegionStart: 0, RegionEnd: 5},
},
write: []interface{}{
2,
"source-version <source> <version-text>",
mustTime(time.Parse(Astronomical, "1997-11-08")),
Sequence{SeqName: "<seqname>", Type: feat.DNA},
linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggctcggattggcgctggatgatagatcagacgac...")), alphabet.DNA),
linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggcucggauuggcgcuggaugauagaucagacgac...")), alphabet.RNA),
linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF...")), alphabet.Protein),
&Region{Sequence: Sequence{SeqName: "<seqname>"}, RegionStart: 0, RegionEnd: 5},
},
},