func main() {
var in1, in2 *fasta.Reader
inName1 := flag.String("1", "", "Filename for first input.")
inName2 := flag.String("2", "", "Filename for second input.")
k := flag.Int("k", 6, "kmer size.")
help := flag.Bool("help", false, "Print this usage message.")
flag.Parse()
if *help {
flag.Usage()
os.Exit(1)
}
var err error
if in1, err = fasta.NewReaderName(*inName1); err != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", err)
os.Exit(0)
}
defer in1.Close()
if in2, err = fasta.NewReaderName(*inName2); err != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", err)
os.Exit(0)
}
defer in2.Close()
var (
seq1, seq2 *seq.Seq
kmerFreqs1, kmerFreqs2 map[kmerindex.Kmer]float64
ok bool
)
if seq1, err = in1.Read(); err != nil {
os.Exit(0)
}
if seq2, err = in2.Read(); err != nil {
os.Exit(0)
}
if index, err := kmerindex.New(*k, seq1); err != nil {
fmt.Println(err)
os.Exit(0)
} else {
if kmerFreqs1, ok = index.NormalisedKmerFrequencies(); !ok {
fmt.Printf("Unable to determine Kmer frequences for %s\n", seq1.ID)
os.Exit(0)
}
}
if index, err := kmerindex.New(*k, seq2); err != nil {
fmt.Println(err)
os.Exit(0)
} else {
if kmerFreqs2, ok = index.NormalisedKmerFrequencies(); !ok {
fmt.Printf("Unable to determine Kmer frequences for %s\n", seq2.ID)
os.Exit(0)
}
}
fmt.Printf("Kmer distance between %s and %s is %f\n", seq1.ID, seq2.ID, kmerindex.Distance(kmerFreqs1, kmerFreqs2))
}
func main() {
var (
in *fasta.Reader
out *os.File
e error
)
inName := flag.String("in", "", "Filename for input. Defaults to stdin.")
outName := flag.String("out", "", "Filename for output. Defaults to stdout.")
k := flag.Int("k", 6, "kmer size.")
start := flag.Int("s", 0, "Start site - mandatory parameter > 0.")
chunk := flag.Int("chunk", 1000, "Chunk width - < 0 indicates sequence to end.")
desch := flag.Bool("desch", false, "Use diagonal base arrangement described by Deschavanne et al., otherwise use orthogonal arrangement.")
help := flag.Bool("help", false, "Print this usage message.")
flag.Parse()
kmerindex.MinKmerLen = *k
if *help {
flag.Usage()
os.Exit(1)
}
if *start == 0 {
fmt.Fprintln(os.Stderr, "Must specify s > 0")
flag.Usage()
os.Exit(0)
}
if *inName == "" {
in = fasta.NewReader(os.Stdin)
} else if in, e = fasta.NewReaderName(*inName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
os.Exit(0)
}
defer in.Close()
if sequence, err := in.Read(); err != nil {
os.Exit(0)
} else {
if *chunk < 0 {
*chunk = sequence.Len() - *start - 1
}
fmt.Fprintf(os.Stderr, "Indexing %s\n", sequence.ID)
if index, err := kmerindex.New(*k, sequence); err != nil {
fmt.Println(err)
os.Exit(0)
} else {
base := color.HSVA{0, 1, 1, 1}
cgr := kmercolor.NewCGR(index, base)
fmt.Fprintf(os.Stderr, "Painting %s\n", sequence.ID)
cgr.Paint(kmercolor.V|kmercolor.H, *desch, *start, *chunk)
fmt.Fprintf(os.Stderr, "Writing %s\n", sequence.ID)
if out, e = os.Create(fmt.Sprintf("%s.png", *outName)); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
}
png.Encode(out, cgr)
out.Close()
}
}
}
func main() {
var (
in *fasta.Reader
out, profile *os.File
e error
)
inName := flag.String("in", "", "Filename for input to be factorised. Defaults to stdin.")
outName := flag.String("out", "", "Filename for output. Defaults to stdout.")
k := flag.Int("k", 8, "kmer size to use.")
cat := flag.Int("cat", 5, "number of categories.")
iter := flag.Int("i", 1000, "iterations.")
limit := flag.Int("time", 10, "time limit for NMF.")
lo := flag.Int("lo", 1, "minimum number of kmer frequency to use in NMF.")
hi := flag.Float64("hi", 0.5, "maximum proportion of kmer representation to use in NMF.")
sf := flag.Float64("sf", 0.01, "factor for sparcity of estimating matrices for NMF.")
tol := flag.Float64("tol", 0.001, "tolerance for NMF.")
threads := flag.Int("threads", 2, "number of threads to use.")
seed := flag.Int64("seed", -1, "seed for random number generator (-1 uses system clock).")
cpuprofile := flag.String("cpuprofile", "", "write cpu profile to this file.")
help := flag.Bool("help", false, "print this usage message.")
flag.Parse()
if *help {
flag.Usage()
os.Exit(1)
}
runtime.GOMAXPROCS(*threads)
sparse.MaxProcs = *threads
fmt.Fprintf(os.Stderr, "Using %d threads.\n", runtime.GOMAXPROCS(0))
if *cpuprofile != "" {
if profile, e = os.Create(*cpuprofile); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
os.Exit(0)
}
fmt.Fprintf(os.Stderr, "Writing CPU profile data to %s\n", *cpuprofile)
pprof.StartCPUProfile(profile)
defer pprof.StopCPUProfile()
}
if *inName == "" {
fmt.Fprintln(os.Stderr, "Reading sequences from stdin.")
in = fasta.NewReader(os.Stdin)
} else if in, e = fasta.NewReaderName(*inName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
os.Exit(0)
} else {
fmt.Fprintf(os.Stderr, "Reading sequence from `%s'.\n", *inName)
}
defer in.Close()
if *outName == "" {
fmt.Fprintln(os.Stderr, "Writing output to stdout.")
out = os.Stdout
} else if out, e = os.Create(*outName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
} else {
fmt.Fprintf(os.Stderr, "Writing output to `%s'.\n", *outName)
}
defer out.Close()
totalkmers := make(map[kmerindex.Kmer]float64)
kmerlists := make([]map[kmerindex.Kmer]float64, 0)
seqTable := make([]string, 0)
for {
if sequence, err := in.Read(); err != nil {
break
} else {
var freqs map[kmerindex.Kmer]float64
if kindex, e := kmerindex.New(*k, sequence); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", e)
fmt.Fprintln(os.Stderr)
os.Exit(0)
} else {
freqs, _ = kindex.NormalisedKmerFrequencies()
kmerlists = append(kmerlists, freqs)
for kmer, freq := range freqs {
totalkmers[kmer] += freq
}
}
seqTable = append(seqTable, string(sequence.ID))
}
}
kmerArray := make([][]float64, 0)
kmerTable := make([]kmerindex.Kmer, 0)
for kmer, _ := range totalkmers {
var count int
for _, kmerlist := range kmerlists {
if kmerlist[kmer] > 0 {
count++
}
}
if count < *lo || float64(count)/float64(len(kmerlists)) > *hi {
continue
}
row := make([]float64, len(kmerlists))
for i, kmerlist := range kmerlists {
row[i] = float64(kmerlist[kmer])
}
kmerArray = append(kmerArray, row)
kmerTable = append(kmerTable, kmer)
}
var kmerMatrix *sparse.Sparse
func() {
defer func() {
if r := recover(); r != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", r)
os.Exit(0)
}
}()
kmerMatrix = sparse.Matrix(kmerArray)
}()
f := func(i, j int, v float64) float64 {
if kmerMatrix.At(i, j) != 0 {
return 1
}
return 0
}
nonZero := kmerMatrix.Apply(f).Sum()
r, c := kmerMatrix.Dims()
density := nonZero / float64(r*c)
if *seed == -1 {
*seed = time.Now().UnixNano()
}
fmt.Fprintf(os.Stderr, "Using %v as random seed.\n", *seed)
rand.Seed(*seed)
rows, cols := kmerMatrix.Dims()
Wo := sparse.Random(rows, *cat, density**sf)
Ho := sparse.Random(*cat, cols, density**sf)
fmt.Fprintf(os.Stderr, "Dimensions of Kmer matrix = (%v, %v)\nDensity = %.3f %%\n%v\n", r, c, (density)*100, kmerMatrix)
W, H, ok := nmf.Factors(kmerMatrix, Wo, Ho, *tol, *iter, time.Duration(*limit)*1e9)
fmt.Fprintf(os.Stderr, "norm(H) = %v norm(W) = %v\n\nFinished = %v\n\n", H.Norm(matrix.Fro), W.Norm(matrix.Fro), ok)
printFeature(out, kmerMatrix, W, H, seqTable, kmerTable, *k)
}
func main() {
var (
in *fasta.Reader
out *fasta.Writer
e error
profile *os.File
)
inName := flag.String("in", "", "Filename for input. Defaults to stdin.")
outName := flag.String("out", "", "Filename for output. Defaults to stdout.")
size := flag.Int("size", 40, "Fragment size.")
width := flag.Int("width", 60, "Fasta output width.")
cpuprofile := flag.String("cpuprofile", "", "write cpu profile to this file.")
help := flag.Bool("help", false, "Print this usage message.")
flag.Parse()
if *help {
flag.Usage()
os.Exit(1)
}
if *cpuprofile != "" {
if profile, e = os.Create(*cpuprofile); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
os.Exit(0)
}
fmt.Fprintf(os.Stderr, "Writing CPU profile data to %s\n", *cpuprofile)
pprof.StartCPUProfile(profile)
defer pprof.StopCPUProfile()
}
if *inName == "" {
in = fasta.NewReader(os.Stdin)
} else if in, e = fasta.NewReaderName(*inName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
}
defer in.Close()
if *outName == "" {
out = fasta.NewWriter(os.Stdout, *width)
} else if out, e = fasta.NewWriterName(*outName, *width); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
}
defer out.Close()
var (
sequence *seq.Seq
err error
)
t := &seq.Seq{}
for {
if sequence, err = in.Read(); err != nil {
break
}
length := sequence.Len()
t.ID = sequence.ID
switch {
case length >= 20 && length <= 85:
t.Seq = sequence.Seq[5:]
out.Write(t)
case length > 85:
for start := 0; start+*size <= length; start += *size {
t.Seq = sequence.Seq[start : start+*size]
out.Write(t)
}
}
}
}
