func main() {
var (
target *gff.Reader
source *gff.Reader
out *gff.Writer
indexFile *os.File
e error
store bool
)
targetName := flag.String("target", "", "Filename for input to be annotated. Defaults to stdin.")
sourceName := flag.String("source", "", "Filename for source annotation.")
indexName := flag.String("index", "", "Filename for index cache.")
outName := flag.String("out", "", "Filename for output. Defaults to stdout.")
flag.Float64Var(&minOverlap, "overlap", 0.05, "Overlap between features.")
threads := flag.Int("threads", 2, "Number of threads to use.")
bufferLen := flag.Int("buffer", 1000, "Length of ouput buffer.")
help := flag.Bool("help", false, "Print this usage message.")
flag.Parse()
runtime.GOMAXPROCS(*threads)
fmt.Fprintf(os.Stderr, "Using %d threads.\n", runtime.GOMAXPROCS(0))
if *help || *sourceName == "" {
flag.Usage()
os.Exit(1)
}
if *targetName == "" {
fmt.Fprintln(os.Stderr, "Reading PALS features from stdin.")
target = gff.NewReader(os.Stdin)
} else if target, e = gff.NewReaderName(*targetName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
os.Exit(0)
} else {
fmt.Fprintf(os.Stderr, "Reading target features from `%s'.\n", *targetName)
}
defer target.Close()
switch {
case *indexName == "" && *sourceName == "":
fmt.Fprintln(os.Stderr, "No source or index provided.")
os.Exit(0)
case *indexName != "" && *sourceName == "":
if indexFile, e = os.Open(*indexName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", e)
os.Exit(0)
}
defer indexFile.Close()
store = false
case *indexName != "" && *sourceName != "":
if indexFile, e = os.Create(*indexName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", e)
os.Exit(0)
}
defer indexFile.Close()
store = true
fallthrough
case *indexName == "" && *sourceName != "":
if source, e = gff.NewReaderName(*sourceName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", e)
os.Exit(0)
}
fmt.Fprintf(os.Stderr, "Reading annotation features from `%s'.\n", *sourceName)
defer source.Close()
}
if *outName == "" {
fmt.Fprintln(os.Stderr, "Writing annotation to stdout.")
out = gff.NewWriter(os.Stdout, 2, 60, false)
} else if out, e = gff.NewWriterName(*outName, 2, 60, true); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
} else {
fmt.Fprintf(os.Stderr, "Writing annotation to `%s'.\n", *outName)
}
defer out.Close()
intervalTree := interval.NewTree()
for count := 0; ; count++ {
if repeat, err := source.Read(); err != nil {
break
} else {
fmt.Fprintf(os.Stderr, "Line: %d\r", count)
repData := &RepeatRecord{}
repData.Parse(repeat.Attributes)
if repInterval, err := interval.New(string(repeat.Location), repeat.Start, repeat.End, 0, *repData); err == nil {
intervalTree.Insert(repInterval)
} else {
fmt.Fprintf(os.Stderr, "Feature has end < start: %v\n", repeat)
}
}
}
process := make(chan *feat.Feature)
buffer := make(chan *feat.Feature, *bufferLen)
processWg := &sync.WaitGroup{}
outputWg := &sync.WaitGroup{}
if *threads < 2 {
*threads = 2
}
for i := 0; i < *threads-1; i++ {
processWg.Add(1)
go processServer(intervalTree, process, buffer, processWg)
}
//output server
outputWg.Add(1)
go func() {
defer outputWg.Done()
for feature := range buffer {
out.Write(feature)
}
}()
for {
if feature, err := target.Read(); err == nil {
process <- feature
} else {
close(process)
break
}
}
if store {
enc := gob.NewEncoder(indexFile)
if e := enc.Encode(intervalTree); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", e)
os.Exit(0)
}
}
processWg.Wait()
close(buffer)
outputWg.Wait()
}
func main() {
var (
region *bed.Reader
motif *bed.Reader
err error
)
motifName := flag.String("motif", "", "Filename for motif file.")
regionName := flag.String("region", "", "Filename for region file.")
verbose := flag.Bool("verbose", false, "Print details of identified motifs to stderr.")
headerLine := flag.Bool("header", false, "Print a header line.")
help := flag.Bool("help", false, "Print this usage message.")
flag.Usage = func() {
fmt.Fprintf(os.Stderr, "Usage: %s -motif <motif file> -region <region file>\n", os.Args[0])
flag.PrintDefaults()
}
flag.Parse()
if *help || *regionName == "" || *motifName == "" {
flag.Usage()
os.Exit(1)
}
// Open files
if motif, err = bed.NewReaderName(*motifName, 3); err != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", err)
os.Exit(0)
} else {
fmt.Fprintf(os.Stderr, "Reading motif features from `%s'.\n", *motifName)
}
defer motif.Close()
if region, err = bed.NewReaderName(*regionName, 3); err != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", err)
os.Exit(0)
} else {
fmt.Fprintf(os.Stderr, "Reading region features from `%s'.\n", *regionName)
}
defer region.Close()
// Read in motif features and build interval tree to search
intervalTree := interval.NewTree()
for line := 1; ; line++ {
if motifLine, err := motif.Read(); err != nil {
break
} else {
if motifInterval, err := interval.New(string(motifLine.Location), motifLine.Start, motifLine.End, 0, nil); err == nil {
intervalTree.Insert(motifInterval)
} else {
fmt.Fprintf(os.Stderr, "Line: %d: Feature has end < start: %v\n", line, motifLine)
}
}
}
// Read in region features and search for motifs within region
// Calculate median motif location, sample standard deviation of locations
// and mean distance of motif from midpoint of region for motifs contained
// within region. Report these and n of motifs within region.
if *headerLine {
fmt.Println("Chromosome\tStart\tEnd\tn-hits\tMeanHitPos\tStddevHitPos\tMeanMidDistance")
}
for line := 1; ; line++ {
if regionLine, err := region.Read(); err != nil {
break
} else {
regionMidPoint := float64(regionLine.Start+regionLine.End) / 2
if regionInterval, err := interval.New(string(regionLine.Location), regionLine.Start, regionLine.End, 0, regionMidPoint); err == nil {
if *verbose {
fmt.Fprintf(os.Stderr, "%s\t%d\t%d\n", regionLine.Location, regionLine.Start, regionLine.End)
}
sumOfDiffs, sumOfSquares, mean, oldmean, n := 0., 0., 0., 0., 0.
for intersector := range intervalTree.Within(regionInterval, 0) {
motifMidPoint := float64(intersector.Start()+intersector.End()) / 2
if *verbose {
fmt.Fprintf(os.Stderr, "\t%s\t%d\t%d\n", intersector.Chromosome(), intersector.Start(), intersector.End())
}
// The Method of Provisional Means
n++
mean = oldmean + (motifMidPoint-oldmean)/n
sumOfSquares += (motifMidPoint - oldmean) * (motifMidPoint - mean)
oldmean = mean
sumOfDiffs += math.Abs(motifMidPoint - regionMidPoint)
}
fmt.Printf("%s\t%d\t%d\t%0.f\t%0.f\t%f\t%f\n",
regionLine.Location, regionLine.Start, regionLine.End,
n, mean, math.Sqrt(sumOfSquares/(n-1)), sumOfDiffs/n)
} else {
fmt.Fprintf(os.Stderr, "Line: %d: Feature has end < start: %v\n", line, regionLine)
}
}
}
}
func (self Alignment) Stitch(f feat.FeatureSet) (a Alignment, err error) {
for _, s := range self {
if !s.Inplace && s.Quality != nil && s.Quality.Inplace {
return nil, bio.NewError("Inplace operation on Quality with non-Inplace operation on parent Seq.", 0, s)
}
}
t := interval.NewTree()
var i *interval.Interval
for _, feature := range f {
if i, err = interval.New("", feature.Start, feature.End, 0, nil); err != nil {
return nil, err
} else {
t.Insert(i)
}
}
start := self.Start()
a = make(Alignment, len(self))
span, err := interval.New("", start, self.End(), 0, nil)
if err != nil {
panic("Seq.End() < Seq.Start()")
}
fs, _ := t.Flatten(span, 0, 0)
var offset int
for i, s := range self {
if s.Inplace {
s.Seq = s.stitch(fs)
if s.Offset -= fs[0].Start(); offset < 0 {
s.Offset = 0
}
s.Circular = false
if s.Quality != nil {
var q *Quality
if s.Quality.Inplace {
q = s.Quality
} else {
q = &Quality{ID: s.Quality.ID}
}
q.Qual = s.Quality.stitch(fs)
if q.Offset = s.Quality.Offset - fs[0].Start(); q.Offset < 0 {
q.Offset = 0
}
q.Circular = false
s.Quality = q
}
a[i] = s
} else {
var q *Quality
if s.Quality != nil {
if offset = s.Quality.Offset - fs[0].Start(); offset < 0 {
offset = 0
}
q = &Quality{
ID: s.Quality.ID,
Qual: s.Quality.stitch(fs),
Offset: offset,
Circular: false,
}
}
if offset = s.Offset - fs[0].Start(); offset < 0 {
offset = 0
}
a[i] = &Seq{
ID: s.ID,
Seq: s.stitch(fs),
Offset: offset,
Strand: s.Strand,
Circular: false,
Moltype: s.Moltype,
Quality: q,
}
}
}
return
}