func main() {
// Parse FASTA from stdin.
fas, err := rosa.ParseFASTA(os.Stdin)
if err != nil {
log.Fatalln(err)
}
// The first sequence in the FASTA file is the DNA sequence and all other
// sequences are introns.
dnaLabel, err := fas.Label(0)
if err != nil {
log.Fatalln(err)
}
dna := fas.Seqs[dnaLabel]
introns := make([]string, len(fas.Seqs)-1)
for label, s := range fas.Seqs {
if label == dnaLabel {
continue
}
introns = append(introns, s)
}
// Splice the DNA, transcribe it into RNA and translate it into a protein.
rna := rosa.Trans(Splice(dna, introns))
prot, err := rosa.Prot(rna)
if err != nil {
log.Fatalln(err)
}
fmt.Println(prot)
}
func main() {
// Get input from stdin.
fas, err := rosa.ParseFASTA(os.Stdin)
if err != nil {
log.Fatalln(err)
}
// The first sequence in the FASTA file is the DNA sequence and the second
// sequence is the subsequence sep.
dnaLabel, err := fas.Label(0)
if err != nil {
log.Fatalln(err)
}
sepLabel, err := fas.Label(1)
if err != nil {
log.Fatalln(err)
}
dna := fas.Seqs[dnaLabel]
sep := fas.Seqs[sepLabel]
// Print the location of each character in sep as a subsequence of dna.
locs := SubSeq(dna, sep)
for i, loc := range locs {
if i != 0 {
fmt.Print(" ")
}
fmt.Print(loc + 1)
}
fmt.Println()
}
func main() {
// Parse FASTA from stdin.
fas, err := rosa.ParseFASTA(os.Stdin)
if err != nil {
log.Fatalln(err)
}
// Locate the DNA sequence with the highest GC-content.
label, gc := MaxGC(fas)
fmt.Println(label)
fmt.Printf("%.6f\n", gc)
}
func ExampleMaxGC() {
// Parse FASTA.
fas, err := rosa.ParseFASTA(strings.NewReader(s))
if err != nil {
log.Fatalln(err)
}
label, gc := MaxGC(fas)
fmt.Println(label)
fmt.Printf("%.6f\n", gc)
// Output:
// Rosalind_0808
// 60.919540
}
func main() {
// Parse FASTA from stdin.
fas, err := rosa.ParseFASTA(os.Stdin)
if err != nil {
log.Fatalln(err)
}
// Create a profile of the provided DNA-sequences and use it to calculate the
// consensus sequence.
var seqs []string
for _, seq := range fas.Seqs {
seqs = append(seqs, seq)
}
profile, err := NewProfile(seqs, true)
if err != nil {
log.Fatalln(err)
}
cons := profile.Cons()
fmt.Println(cons)
}
func main() {
// Parse FASTA from stdin.
fas, err := rosa.ParseFASTA(os.Stdin)
if err != nil {
log.Fatalln(err)
}
// Locate the single DNA sequence present in the FASTA file.
label, err := fas.Label(0)
if err != nil {
log.Fatalln(err)
}
dna := fas.Seqs[label]
// Calculate the length and locating of each reverse palindrome within the
// DNA sequence which has a length of between 4 and 12 nucleotides.
locs, ns := RevPal(dna)
for i := range locs {
loc := locs[i]
n := ns[i]
fmt.Println(loc+1, n)
}
}
func main() {
// Parse FASTA from stdin.
fas, err := rosa.ParseFASTA(os.Stdin)
if err != nil {
log.Fatalln(err)
}
label, err := fas.Label(0)
if err != nil {
log.Fatalln(err)
}
dna := fas.Seqs[label]
revc := rosa.RevComp(dna)
// Locates each open reading frame (ORF) of the DNA-sequence and its reverse
// complement. Use a map for the store unique proteins.
orfs := ORFs(dna)
orfs = append(orfs, ORFs(revc)...)
uniq := make(map[string]bool)
for _, orf := range orfs {
rna := rosa.Trans(orf)
prot, err := rosa.Prot(rna)
if err != nil {
log.Fatalln(err)
}
uniq[prot] = true
}
// Print sorted proteins.
var prots []string
for prot := range uniq {
prots = append(prots, prot)
}
sort.Strings(prots)
for _, prot := range prots {
fmt.Println(prot)
}
}