Reputation: 817
I am working on creating a k-mer frequency counter (similar to word count in Hadoop) written in Scala. I'm fairly new to Scala, but I have some programming experience.
The input is a text file containing a gene sequence and my task is to get the frequency of each k-mer where k
is some specified length of the sequence.
Therefore, the sequence AGCTTTC
has three 5-mers (AGCTT, GCTTT, CTTTC)
I've parsed through the input and created a huge string which is the entire sequence, the new lines throw off the k-mer counting as the end of one line's sequence should still form a k-mer with the beginning of the next line's sequence.
Now I am trying to write a function that will generate a list of maps List[Map[String, Int]]
with which it should be easy to use scala's groupBy
function to get the count of the common k-mers
import scala.io.Source
object Main {
def main(args: Array[String]) {
// Get all of the lines from the input file
val input = Source.fromFile("input.txt").getLines.toArray
// Create one huge string which contains all the lines but the first
val lines = input.tail.mkString.replace("\n","")
val mappedKmers: List[Map[String,Int]] = getMappedKmers(5, lines)
}
def getMappedKmers(k: Int, seq: String): List[Map[String, Int]] = {
for (i <- 0 until seq.length - k) {
Map(seq.substring(i, i+k), 1) // Map the k-mer to a count of 1
}
}
}
Couple of questions:
List[Map[String,Int]]
?Any help and/or advice is definitely appreciated!
Upvotes: 4
Views: 436
Reputation: 139028
You're pretty close—there are three fairly minor problems with your code.
The first is that for (i <- whatever) foo(i)
is syntactic sugar for whatever.foreach(i => foo(i))
, which means you're not actually doing anything with the contents of whatever
. What you want is for (i <- whatever) yield foo(i)
, which is sugar for whatever.map(i => foo(i))
and returns the transformed collection.
The second issue is that 0 until seq.length - k
is a Range
, not a List
, so even once you've added the yield
, the result still won't line up with the declared return type.
The third issue is that Map(k, v)
tries to create a map with two key-value pairs, k
and v
. You want Map(k -> v)
or Map((k, v))
, either of which is explicit about the fact that you have a single argument pair.
So the following should work:
def getMappedKmers(k: Int, seq: String): IndexedSeq[Map[String, Int]] = {
for (i <- 0 until seq.length - k) yield {
Map(seq.substring(i, i + k) -> 1) // Map the k-mer to a count of 1
}
}
You could also convert either the range or the entire result to a list with .toList
if you'd prefer a list at the end.
It's worth noting, by the way, that the sliding
method on Seq
does exactly what you want:
scala> "AGCTTTC".sliding(5).foreach(println)
AGCTT
GCTTT
CTTTC
I'd definitely suggest something like "AGCTTTC".sliding(5).toList.groupBy(identity)
for real code.
Upvotes: 4