Function for returning a list of cards when repeating by line, number of counters
I am working on creating a k-mer frequency counter (similar to word counting in Hadoop) written in Scala. I'm new to Scala, but I have some programming experience.
Input is a text file containing a sequence of genes, and my task is to get the frequency of each k-mer, where k
is the specific length of the sequence.
Hence the sequence AGCTTTC
has three 5-dimensional (AGCTT, GCTTT, CTTTC)
I parsed the input and created a huge line that represents the entire sequence, newlines discard the k-mer count as the end of one line should still form a k-mer with the start of the next sequence of lines.
Now I am trying to write a function that will generate a list of cards List[Map[String, Int]]
with which it should be easy to use a scala function groupBy
to get a counter of the total 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
}
}
}
A couple of questions:
- How to create / generate
List[Map[String,Int]]
? - How do you do it?
Any help and / or advice is definitely appreciated!
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You're pretty close - there are three fairly minor issues with your code.
The first for (i <- whatever) foo(i)
is syntactic sugar for whatever.foreach(i => foo(i))
, which means you don't actually do anything with the content whatever
. You want for (i <- whatever) yield foo(i)
which is sugar for whatever.map(i => foo(i))
and returns the converted collection.
The second problem is what 0 until seq.length - k
is Range
, and not List
, so even after adding, the yield
result will still not match the declared return type.
The third problem is Map(k, v)
trying to create a map with two key-value pairs, k
and v
. You want Map(k -> v)
or Map((k, v))
, each of which explicitly indicates that you have one pair of arguments.
This is how 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 can also convert the range or the entire result to a list with .toList
if you prefer a list at the end.
It is worth noting, incidentally, that the method sliding
to Seq
doing exactly what you want:
scala> "AGCTTTC".sliding(5).foreach(println)
AGCTT
GCTTT
CTTTC
I would definitely suggest something like "AGCTTTC".sliding(5).toList.groupBy(identity)
for real code.
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