From e6527f3b9bba508b294891e2e5a759033ee59355 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Aug 2014 14:13:05 +0200
Subject: [PATCH] Finalize summary structure
---
.../flexiprep/FlexiprepSummary.scala | 84 +++++++++++--------
1 file changed, 48 insertions(+), 36 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
index 915c17fcc..fc831fcd0 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
@@ -1,5 +1,6 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
+import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Sha1sum
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.{ FastqSync, Seqstat }
@@ -46,6 +47,8 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
var fastqcR2after: Fastqc = _
var flexiprep: Flexiprep = root.asInstanceOf[Flexiprep]
+
+ var resourses:Map[String, Json] = Map()
def addFastqc(fastqc: Fastqc, R2: Boolean = false, after: Boolean = false): Fastqc = {
if (!R2 && !after) this.fastqcR1 = fastqc
@@ -99,29 +102,39 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
// format: OFF
override def run {
logger.debug("Start")
+ sha1Summary()
val summary =
- ("flexiprep" := (
- ("clipping" := !flexiprep.skipClip) ->:
- ("trimming" := !flexiprep.skipTrim) ->:
- ("paired" := flexiprep.paired) ->:
- jEmptyObject)) ->:
- ("seqstat" := seqstatSummary) ->:
- ("sha1" := sha1Summary) ->:
- ("fastqc" := fastqcSummary) ->:
- ("clipping" :=? clipstatSummary) ->?:
- ("trimming" :=? trimstatSummary) ->?:
- jEmptyObject
+ ("samples" := ( flexiprep.sampleName :=
+ ("runs" := ( flexiprep.libraryName := (
+ ("flexiprep" := (
+ ("clipping" := !flexiprep.skipClip) ->:
+ ("trimming" := !flexiprep.skipTrim) ->:
+ ("paired" := flexiprep.paired) ->:
+ jEmptyObject)) ->:
+ ("stats" := (
+ ("fastq" := seqstatSummary) ->:
+ ("clipping" :=? clipstatSummary) ->?:
+ ("trimming" :=? trimstatSummary) ->?:
+ jEmptyObject)) ->:
+ ("resourses" := (("raw_R1" := getResourses(fastqcR1, sha1R1)) ->:
+ ("raw_R2" :?= getResourses(fastqcR2, sha1R2)) ->?:
+ ("proc_R1" :?= getResourses(fastqcR1after, sha1R1after)) ->?:
+ ("proc_R2" :?= getResourses(fastqcR2after, sha1R2after)) ->?:
+ jEmptyObject)) ->:
+ jEmptyObject ))->: jEmptyObject)->: jEmptyObject)->: jEmptyObject) ->: jEmptyObject
// format: ON
- logger.debug(summary.spaces2) // TODO: need output writter
+ val summeryText = summary.spaces2
+ logger.debug("\n" + summeryText)
+ val writer = new PrintWriter(out)
+ writer.write(summeryText)
+ writer.close()
logger.debug("Stop")
}
def seqstatSummary(): Option[Json] = {
- val R1: Json = if (chunks.size == 1) chunks.head._2.seqstatR1.getSummary
- else {
- val s = for ((key, value) <- chunks) yield value.seqstatR1.getSummary
- Seqstat.mergeSummarys(s.toList)
- }
+ val R1_chunks = for ((key, value) <- chunks) yield value.seqstatR1.getSummary
+ val R1: Json = Seqstat.mergeSummarys(R1_chunks.toList)
+
val R2: Option[Json] = if (!flexiprep.paired) None
else if (chunks.size == 1) Option(chunks.head._2.seqstatR2.getSummary)
else {
@@ -147,12 +160,16 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
jEmptyObject)
}
- def sha1Summary: Json = {
- return ("R1_raw" := sha1Summary(sha1R1)) ->:
- ("R2_raw" :=? sha1Summary(sha1R2)) ->?:
- ("R1_proc" :=? sha1Summary(sha1R1after)) ->?:
- ("R2_proc" :=? sha1Summary(sha1R2after)) ->?:
- jEmptyObject
+ def sha1Summary() {
+ val R1_raw = sha1Summary(sha1R1)
+ val R2_raw = sha1Summary(sha1R2)
+ val R1_proc = sha1Summary(sha1R1after)
+ val R2_proc = sha1Summary(sha1R2after)
+
+ if (!R1_raw.isEmpty) resourses += ("fastq_R1_raw" -> R1_raw.get)
+ if (!R2_raw.isEmpty) resourses += ("fastq_R2_raw" -> R2_raw.get)
+ if (!R1_proc.isEmpty) resourses += ("fastq_R1_proc" -> R1_proc.get)
+ if (!R2_proc.isEmpty) resourses += ("fastq_R2_proc" -> R2_proc.get)
}
def sha1Summary(sha1sum: Sha1sum): Option[Json] = {
@@ -160,14 +177,12 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
else return Option(sha1sum.getSummary)
}
- def fastqcSummary: Json = {
- return ("R1_raw" := fastqcSummary(fastqcR1)) ->:
- ("R2_raw" :=? fastqcSummary(fastqcR2)) ->?:
- ("R1_proc" :=? fastqcSummary(fastqcR1after)) ->?:
- ("R2_proc" :=? fastqcSummary(fastqcR2after)) ->?:
- jEmptyObject
+ def getResourses(fastqc:Fastqc, sha1sum:Sha1sum): Option[Json] = {
+ if (fastqc == null || sha1sum == null) return None
+ val fastqcSum = fastqcSummary(fastqc).get
+ return Option(("fastq" := sha1Summary(sha1sum)) ->: fastqcSum)
}
-
+
def fastqcSummary(fastqc: Fastqc): Option[Json] = {
if (fastqc == null) return None
else return Option(fastqc.getSummary)
@@ -188,17 +203,14 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
}
return Option(("R1" := R1) ->:
("R2" :=? R2) ->?:
- ("fastqSync" :=? syncstatSummary) ->?:
+ ("fastq_sync" :=? syncstatSummary) ->?:
jEmptyObject)
}
def syncstatSummary(): Option[Json] = {
if (flexiprep.skipClip || !flexiprep.paired) return None
- if (chunks.size == 1) return Option(chunks.head._2.sickle.getSummary)
- else {
- val s = for ((key, value) <- chunks) yield value.fastqSync.getSummary
- return Option(FastqSync.mergeSummarys(s.toList))
- }
+ val s = for ((key, value) <- chunks) yield value.fastqSync.getSummary
+ return Option(FastqSync.mergeSummarys(s.toList))
}
def trimstatSummary(): Option[Json] = {
--
GitLab