source code
/* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
contributed by Ralph Ganszky
modified by Michael Morrell
No match for key (for example "GGTATTTTAATT") causes --
"fatal error: unexpectedly found nil while unwrapping an Optional value"
*/
import Glibc
import Dispatch
let ENABLED_THREAD_COUNT = 4
let ntasks = ENABLED_THREAD_COUNT
let mQueue = DispatchQueue(label: "mergeQueue")
func compress(_ seq: ArraySlice<UInt8>) -> Int {
var res = 0
for i in seq.indices {
res = (res << 2) | Int(seq[i])
}
return res
}
func getSequenceHash(_ n: Int, seq: [UInt8]) -> [Int:Int] {
var hash = [Int:Int]()
let slice = (seq.count-(n-1)) / ntasks
let remainder = (seq.count-(n-1)) % ntasks
let mask = n > 1 ? ((1 << (2*(n-1))) - 1) : 0
DispatchQueue.concurrentPerform(iterations: ntasks) { i in
var lHash = [Int:Int](minimumCapacity: 1 << min(n, 12))
var idx = compress(seq[i*slice..<i*slice+n])
lHash[idx] = (lHash[idx] ?? 0) + 1
let startIdx = i*slice+n
let endIdx = startIdx + slice - 1
for l in startIdx..<endIdx {
idx = ((idx & mask) << 2) | Int(seq[l])
lHash[idx] = (lHash[idx] ?? 0) + 1
}
mQueue.sync {
for (key, value) in lHash {
hash[key] = (hash[key] ?? 0) + value
}
}
}
let startIdx = seq.count - remainder - (n - 1)
let endIdx = seq.count - (n - 1)
for i in startIdx..<endIdx {
let idx = compress(seq[i..<i+n])
hash[idx] = (hash[idx] ?? 0) + 1
}
return hash
}
let c2i: [Character:Int] = [ "A": 0, "C": 1, "T": 2, "G": 3 ]
func encode(_ seq: String) -> Int {
let cSeq = seq.characters
var res = 0
for c in cSeq {
res = res << 2 | c2i[c]!
}
return res
}
func roundDouble(_ num: Double, precision: Int) -> String {
let exponent = pow(10.0, Double(precision))
let number = Double(Int(num * exponent + 0.5)) / exponent
var numberStr = "\(number)"
while numberStr.characters.count < Int(log10(num)) + 2 + precision {
numberStr = numberStr + "0"
}
return numberStr
}
func readInput() -> [UInt8] {
var seq = [UInt8]()
let pattern = ">THREE Homo sapiens frequency"
while let line = readLine() {
if line == pattern {
break
}
}
while let line = readLine() {
seq += Array(line.utf8)
}
return seq
}
// Read sequence
var sequence = readInput()
// rewrite bytes with 2bit code
for i in 0..<sequence.count {
sequence[i] = (sequence[i] & 0x6) >> 1
}
let hash = getSequenceHash(1, seq: sequence)
let i2c = [ 0: "A", 1: "C", 2: "T", 3: "G" ]
let total = hash.reduce(0) { $0 + $1.1 }
for k in hash.keys.sorted(by: {hash[$1]! < hash[$0]!}) {
print("\(i2c[k]!) \(roundDouble(100.0*Double(hash[k]!)/Double(total), precision: 3))")
}
print()
let hash2 = getSequenceHash(2, seq: sequence)
let total2 = hash2.reduce(0) { $0 + $1.1 }
for k in hash2.keys.sorted(by: {hash2[$1]! < hash2[$0]!}) {
print("\(i2c[k>>2]!)\(i2c[k&3]!) \(roundDouble(100.0*Double(hash2[k]!)/Double(total2), precision: 3))")
}
print()
let hash3 = getSequenceHash(3, seq: sequence)
print("\(hash3[encode("GGT")]!)\tGGT")
let hash4 = getSequenceHash(4, seq: sequence)
print("\(hash4[encode("GGTA")]!)\tGGTA")
let hash6 = getSequenceHash(6, seq: sequence)
print("\(hash6[encode("GGTATT")]!)\tGGTATT")
let hash12 = getSequenceHash(12, seq: sequence)
print("\(hash12[encode("GGTATTTTAATT")]!)\tGGTATTTTAATT")
let hash18 = getSequenceHash(18, seq: sequence)
print("\(hash18[encode("GGTATTTTAATTTATAGT")]!)\tGGTATTTTAATTTATAGT")