From 45b54bc61d4bc52c4d7998b03b15ba690fdcc52a Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 1 Oct 2015 16:06:47 +0200
Subject: [PATCH] Simplified tree management
---
.../biopet/tools/KrakenReportToJson.scala | 115 ++++++------------
1 file changed, 34 insertions(+), 81 deletions(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
index 580eb0e00..ed5b1f028 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
@@ -23,6 +23,7 @@ import java.io.{ PrintWriter, File }
import nl.lumc.sasc.biopet.utils.ConfigUtils._
import nl.lumc.sasc.biopet.utils.ToolCommand
+import scala.collection.mutable.ListBuffer
import scala.collection.{ immutable, mutable }
import scala.io.Source
@@ -34,9 +35,9 @@ case class KrakenHit(taxonomyID: Long,
taxonRank: String,
cladeLevel: Int,
parentTaxonomyID: Long,
- children: List[KrakenHit]) {
+ children: ListBuffer[KrakenHit]) {
def toJSON(): Map[String, Any] = {
- val childJSON = children.map(entry => entry.toJSON())
+ val childJSON = children.toList.map(entry => entry.toJSON())
Map(
"name" -> taxonomyName,
"taxid" -> taxonomyID,
@@ -84,53 +85,33 @@ object KrakenReportToJson extends ToolCommand {
.parse(args, Args())
.getOrElse(sys.exit(1))
- def mergeBranch(branchA: Map[Long, KrakenHit],
- branchB: KrakenHit): KrakenHit = {
- var brA = branchA.head._2
- var children = branchB.children
- var cladeCount = branchB.cladeCount
- var cladeSize = branchB.cladeSize
+ def parseLine( krakenRawHit: String ): Map[Long, KrakenHit] = {
+ val values: Array[String] = krakenRawHit.stripLineEnd.split("\t")
+ val scientificName: String = values(5)
+ val cladeLevel = spacePattern.findFirstIn(scientificName).getOrElse("").length / 2
- /* special case for the root node */
- if (brA.taxonomyID == branchB.taxonomyID) {
- cladeCount = brA.cladeCount
- cladeSize = brA.cladeSize
-
- }
-
- /* determine to scan in branchB or return Map containing a because we cannot merge? */
- if (brA.cladeLevel > branchB.cladeLevel) {
- /* if brA's cladelevel is deeper than branchB, work on the children if any when it doesn't match it as parent */
-
- if (brA.parentTaxonomyID == branchB.taxonomyID) {
- children :+= brA
- } else {
- /* extend in its children */
- // TODO: do preliminary escape, don't check deeper in the tree when we have a hit.
- children = children.map(child => {
- mergeBranch(branchA, child)
- })
- }
- } else {
- /* Hits are on the same level(have siblings, adding to parent) */
+ if (cladeIDs.length <= cladeLevel + 1) {
+ cladeIDs ++= mutable.ArrayBuffer.fill(10)(0L)
}
- new KrakenHit(
- taxonomyID = branchB.taxonomyID,
- taxonomyName = branchB.taxonomyName,
- cladeCount = cladeCount,
- cladeSize = cladeSize,
- taxonRank = branchB.taxonRank,
- cladeLevel = branchB.cladeLevel,
- parentTaxonomyID = branchB.parentTaxonomyID,
- children = children
- )
+ cladeIDs(cladeLevel + 1) = values(4).toLong
+ Map(
+ values(4).toLong -> new KrakenHit(
+ taxonomyID = values(4).toLong,
+ taxonomyName = scientificName.trim,
+ cladeCount = values(2).toLong,
+ cladeSize = values(1).toLong,
+ taxonRank = values(3),
+ cladeLevel = cladeLevel,
+ parentTaxonomyID = cladeIDs(cladeLevel),
+ children = ListBuffer()
+ ))
}
def reportToJson(reportRaw: File): String = {
val reader = Source.fromFile(reportRaw)
- val lines = reader.getLines().toList.filter(!_.isEmpty)
+// val lines = reader.getLines().toList.filter(!_.isEmpty)
/*
* http://ccb.jhu.edu/software/kraken/MANUAL.html
@@ -143,48 +124,20 @@ object KrakenReportToJson extends ToolCommand {
* 6. indented scientific name
* */
- /*
- * Entries will be formatted to:
- * entries[ <taxid> ] = Map( <taxid>, Map(...))
- * */
- val entries: List[Map[Long, KrakenHit]] = for (tsvLine <- lines.tail) yield {
- val values = tsvLine.split("\t")
- val scientificName: String = values(5)
- val cladeLevel = spacePattern.findFirstIn(scientificName).getOrElse("").length / 2
+ val lines = reader.getLines()
+ .map(line => parseLine(line))
+ .filter(p => p.head._2.cladeSize > 0)
+ .foldLeft(Map.empty[Long, KrakenHit])( (a,b) => {
+ a + b.head
+ } )
- if (cladeIDs.length <= cladeLevel + 1) {
- cladeIDs ++= mutable.ArrayBuffer.fill(10)(0L)
- }
+ lines.keys.foreach(k => {
+ // append itself to the children attribute of the parent
+ lines(lines(k).parentTaxonomyID).children += lines(k)
+ })
+
+ mapToJson(lines(1).toJSON()).spaces2
- cladeIDs(cladeLevel + 1) = values(4).toLong
- Map(
- values(4).toLong -> new KrakenHit(
- taxonomyID = values(4).toLong,
- taxonomyName = scientificName.trim,
- cladeCount = values(2).toLong,
- cladeSize = values(1).toLong,
- taxonRank = values(3),
- cladeLevel = cladeLevel,
- parentTaxonomyID = cladeIDs(cladeLevel),
- children = List()
- ))
- }
- val mm: KrakenHit = entries.foldLeft(
- new KrakenHit(
- taxonomyID = 1L,
- taxonomyName = "root",
- cladeCount = 0L,
- cladeSize = 0L,
- taxonRank = "-",
- cladeLevel = 0,
- parentTaxonomyID = 0L,
- children = List()
- )) { (bb: KrakenHit, aa: Map[Long, KrakenHit]) =>
- {
- mergeBranch(aa, bb)
- }
- }
- mapToJson(mm.toJSON()).spaces2
}
def main(args: Array[String]): Unit = {
--
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