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 ExampleORFs() {
dna := "AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG"
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)
}
// Output:
// M
// MGMTPRLGLESLLE
// MLLGSFRLIPKETLIQVAGSSPCNLS
// MTPRLGLESLLE
}
func main() {
// Get input from stdin.
buf, err := ioutil.ReadAll(os.Stdin)
if err != nil {
log.Fatalln(err)
}
dna := string(buf)
// Transcribe the DNA sequence into an RNA sequence.
fmt.Println(rosa.Trans(dna))
}
func ExampleSplc() {
// Splice the DNA, transcribe it into RNA and translate it into a protein.
dna := "ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG"
introns := []string{"ATCGGTCGAA", "ATCGGTCGAGCGTGT"}
rna := rosa.Trans(Splice(dna, introns))
prot, err := rosa.Prot(rna)
if err != nil {
log.Fatalln(err)
}
fmt.Println(prot)
// Output: MVYIADKQHVASREAYGHMFKVCA
}
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)
}
}