Bioinformatics/Sequence mutation: Difference between revisions
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T: 45</pre>
=={{header|Vlang}}==
{{trans|Go}}
<lang vlang>import rand
import rand.seed
const bases = "ACGT"
// 'w' contains the weights out of 300 for each
// of swap, delete or insert in that order.
fn mutate(dna string, w [3]int) string {
le := dna.len
// get a random position in the dna to mutate
p := rand.intn(le) or {0}
// get a random number between 0 and 299 inclusive
r := rand.intn(300) or {0}
mut bytes := dna.bytes()
match true {
r < w[0] { // swap
base := bases[rand.intn(4) or {0}]
println(" Change @${p:3} ${[bytes[p]].bytestr()} to ${[base].bytestr()}")
bytes[p] = base
}
r < w[0]+w[1] { // delete
println(" Delete @${p:3} ${bytes[p]}")
bytes.delete(p)
//copy(bytes[p:], bytes[p+1:])
bytes = bytes[0..le-1]
}
else { // insert
base := bases[rand.intn(4) or {0}]
bytes << 0
bytes.insert(p,bytes[p])
//copy(bytes[p+1:], bytes[p:])
println(" Insert @${p:3} $base")
bytes[p] = base
}
}
return bytes.bytestr()
}
// Generate a random dna sequence of given length.
fn generate(le int) string {
mut bytes := []u8{len:le}
for i := 0; i < le; i++ {
bytes[i] = bases[rand.intn(4) or {0}]
}
return bytes.bytestr()
}
// Pretty print dna and stats.
fn pretty_print(dna string, rowLen int) {
println("SEQUENCE:")
le := dna.len
for i := 0; i < le; i += rowLen {
mut k := i + rowLen
if k > le {
k = le
}
println("${i:5}: ${dna[i..k]}")
}
mut base_map := map[byte]int{} // allows for 'any' base
for i in 0..le {
base_map[dna[i]]++
}
mut bb := base_map.keys()
bb.sort()
println("\nBASE COUNT:")
for base in bb {
println(" $base: ${base_map[base]:3}")
}
println(" ------")
println(" Σ: $le")
println(" ======\n")
}
// Express weights as a string.
fn wstring(w [3]int) string {
return " Change: ${w[0]}\n Delete: ${w[1]}\n Insert: ${w[2]}\n"
}
fn main() {
rand.seed(seed.time_seed_array(2))
mut dna := generate(250)
pretty_print(dna, 50)
muts := 10
w := [100, 100, 100]! // use e.g. {0, 300, 0} to choose only deletions
println("WEIGHTS (ex 300):\n${wstring(w)}")
println("MUTATIONS ($muts):")
for _ in 0..muts {
dna = mutate(dna, w)
}
println('')
pretty_print(dna, 50)
}</lang>
{{out}}
Sample run:
<pre>
SEQUENCE:
0: CATTGGATTGCTAGTCGTTCAATAGCGAACGAACAGTTTGCATGAATCAG
50: AGAGAGCCTGAAACCTTGGTTGGTATCGACACAACCTCATAATTCACATT
100: CACAAACTTATTTTCGGATCCGCGAAAACGCAAGCGCATTAAGAGACACC
150: CCCAGAGACTCAATTCCGGATTTGCGCTGCTATATACCCACATTGATGAT
200: ATAGGGCTTAGAACGGCCTTAGCCCCGTCGGCTAGTTTCTGAAGTCTCTT
BASE COUNT:
A: 71
C: 62
G: 52
T: 65
------
Σ: 250
======
WEIGHTS (ex 300):
Change: 100
Delete: 100
Insert: 100
MUTATIONS (10):
Delete @166 "C"
Change @185 "C" to "G"
Insert @230 "T"
Insert @230 "G"
Insert @226 "C"
Change @162 "A" to "C"
Change @236 "G" to "C"
Insert @ 25 "C"
Delete @ 75 "A"
Change @104 "A" to "T"
SEQUENCE:
0: CATTGGATTGCTAGTCGTTCAATAGCCGAACGAACAGTTTGCATGAATCA
50: GAGAGAGCCTGAAACCTTGGTTGGTTCGACACAACCTCATAATTCACATT
100: CACATACTTATTTTCGGATCCGCGAAAACGCAAGCGCATTAAGAGACACC
150: CCCAGAGACTCACTTCGGATTTGCGCTGCTATATAGCCACATTGATGATA
200: TAGGGCTTAGAACGGCCTTAGCCCCGCTCGGGTCTACTTTCTGAAGTCTC
250: TT
BASE COUNT:
A: 68
C: 64
G: 53
T: 67
------
Σ: 252
======
</pre>
=={{header|Wren}}==
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