From f6791cc08d6bccd3f607be69a74dc30745a2b3a4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 13:09:59 +0100
Subject: [PATCH] Remove old summary code
---
.../lumc/sasc/biopet/extensions/Seqstat.scala | 67 -----
.../nl/lumc/sasc/biopet/tools/FastqSync.scala | 50 ----
.../biopet/pipelines/flexiprep/Cutadapt.scala | 51 ----
.../biopet/pipelines/flexiprep/Fastqc.scala | 30 ---
.../pipelines/flexiprep/Flexiprep.scala | 40 +--
.../flexiprep/FlexiprepSummary.scala | 242 ------------------
.../biopet/pipelines/flexiprep/Sickle.scala | 47 ----
7 files changed, 5 insertions(+), 522 deletions(-)
delete mode 100644 public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
index c7c1a4436..a8bf55177 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
@@ -45,12 +45,6 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction with Sum
def cmdLine = required(executable) + required(input) + " > " + required(output)
- def getSummary: Json = {
- val json = Parse.parseOption(Source.fromFile(output).mkString)
- if (json.isEmpty) return jNull
- else return json.get.fieldOrEmptyObject("stats")
- }
-
def summaryData: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
@@ -79,65 +73,4 @@ object Seqstat {
seqstat.output = new File(outDir + fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
return seqstat
}
-
- def mergeSummaries(jsons: List[Json]): Json = {
- def addJson(json: Json, total: mutable.Map[String, Long]) {
- for (key <- json.objectFieldsOrEmpty) {
- if (json.field(key).get.isObject) addJson(json.field(key).get, total)
- else if (json.field(key).get.isNumber) {
- val number = json.field(key).get.numberOrZero.toLong
- if (total.contains(key)) {
- if (key == "len_min") {
- if (total(key) > number) total(key) = number
- } else if (key == "len_max") {
- if (total(key) < number) total(key) = number
- } else total(key) += number
- } else total += (key -> number)
- }
- }
- }
-
- var basesTotal: mutable.Map[String, Long] = mutable.Map()
- var readsTotal: mutable.Map[String, Long] = mutable.Map()
- var encoding: Set[Json] = Set()
- for (json <- jsons) {
- encoding += json.fieldOrEmptyString("qual_encoding")
-
- val bases = json.fieldOrEmptyObject("bases")
- addJson(bases, basesTotal)
-
- val reads = json.fieldOrEmptyObject("reads")
- addJson(reads, readsTotal)
- }
- return ("bases" := (
- ("num_n" := basesTotal("num_n")) ->:
- ("num_total" := basesTotal("num_total")) ->:
- ("num_qual_gte" := (
- ("1" := basesTotal("1")) ->:
- ("10" := basesTotal("10")) ->:
- ("20" := basesTotal("20")) ->:
- ("30" := basesTotal("30")) ->:
- ("40" := basesTotal("40")) ->:
- ("50" := basesTotal("50")) ->:
- ("60" := basesTotal("60")) ->:
- jEmptyObject
- )) ->: jEmptyObject)) ->:
- ("reads" := (
- ("num_with_n" := readsTotal("num_with_n")) ->:
- ("num_total" := readsTotal("num_total")) ->:
- ("len_min" := readsTotal("len_min")) ->:
- ("len_max" := readsTotal("len_max")) ->:
- ("num_mean_qual_gte" := (
- ("1" := readsTotal("1")) ->:
- ("10" := readsTotal("10")) ->:
- ("20" := readsTotal("20")) ->:
- ("30" := readsTotal("30")) ->:
- ("40" := readsTotal("40")) ->:
- ("50" := readsTotal("50")) ->:
- ("60" := readsTotal("60")) ->:
- jEmptyObject
- )) ->: jEmptyObject)) ->:
- ("qual_encoding" := encoding.head) ->:
- jEmptyObject
- }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 9c11d1519..f47eeb300 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -105,32 +105,6 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction wi
case _ => v1
}
}
-
- // summary statistics
- def summary: Json = {
-
- val regex = new Regex("""Filtered (\d*) reads from first read file.
- |Filtered (\d*) reads from second read file.
- |Synced read files contain (\d*) reads.""".stripMargin,
- "R1", "R2", "RL")
-
- val (countFilteredR1, countFilteredR2, countRLeft) =
- if (outputStats.exists) {
- val text = Source
- .fromFile(outputStats)
- .getLines()
- .mkString("\n")
- regex.findFirstMatchIn(text) match {
- case None => (0, 0, 0)
- case Some(rmatch) => (rmatch.group("R1").toInt, rmatch.group("R2").toInt, rmatch.group("RL").toInt)
- }
- } else (0, 0, 0)
-
- ("num_reads_discarded_R1" := countFilteredR1) ->:
- ("num_reads_discarded_R2" := countFilteredR2) ->:
- ("num_reads_kept" := countRLeft) ->:
- jEmptyObject
- }
}
object FastqSync extends ToolCommand {
@@ -210,30 +184,6 @@ object FastqSync extends ToolCommand {
(numDiscA, numDiscB, numKept)
}
- /** Function to merge this tool's summary with summaries from other objects */
- // TODO: refactor this into the object? At least make it work on the summary object
- def mergeSummaries(jsons: List[Json]): Json = {
-
- val (read1FilteredCount, read2FilteredCount, readsLeftCount) = jsons
- // extract the values we require from each JSON object into tuples
- .map {
- case json =>
- (json.field("num_reads_discarded_R1").get.numberOrZero.toInt,
- json.field("num_reads_discarded_R2").get.numberOrZero.toInt,
- json.field("num_reads_kept").get.numberOrZero.toInt)
- }
- // reduce the tuples
- .reduceLeft {
- (x: (Int, Int, Int), y: (Int, Int, Int)) =>
- (x._1 + y._1, x._2 + y._2, x._3 + y._3)
- }
-
- ("num_reads_discarded_R1" := read1FilteredCount) ->:
- ("num_reads_discarded_R2" := read2FilteredCount) ->:
- ("num_reads_kept" := readsLeftCount) ->:
- jEmptyObject
- }
-
case class Args(refFastq: File = new File(""),
inputFastq1: File = new File(""),
inputFastq2: File = new File(""),
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
index 15996cbe7..564bb4427 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -86,31 +86,6 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
}
def summaryFiles: Map[String, File] = Map("input" -> fastq_input, "output" -> fastq_output)
-
- def getSummary: Json = {
- val trimR = """.*Trimmed reads: *(\d*) .*""".r
- val tooShortR = """.*Too short reads: *(\d*) .*""".r
- val tooLongR = """.*Too long reads: *(\d*) .*""".r
- val adapterR = """Adapter '([C|T|A|G]*)'.*trimmed (\d*) times.""".r
-
- var stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
- var adapter_stats: mutable.Map[String, Int] = mutable.Map()
-
- if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines) {
- line match {
- case trimR(m) => stats += ("trimmed" -> m.toInt)
- case tooShortR(m) => stats += ("tooshort" -> m.toInt)
- case tooLongR(m) => stats += ("toolong" -> m.toInt)
- case adapterR(adapter, count) => adapter_stats += (adapter -> count.toInt)
- case _ =>
- }
- }
- return ("num_reads_affected" := stats("trimmed")) ->:
- ("num_reads_discarded_too_short" := stats("tooshort")) ->:
- ("num_reads_discarded_too_long" := stats("toolong")) ->:
- ("adapters" := adapter_stats.toMap) ->:
- jEmptyObject
- }
}
object Cutadapt {
@@ -121,30 +96,4 @@ object Cutadapt {
cutadapt.stats_output = new File(output.getAbsolutePath.substring(0, output.getAbsolutePath.lastIndexOf(".")) + ".stats")
return cutadapt
}
-
- def mergeSummaries(jsons: List[Json]): Json = {
- var affected = 0
- var tooShort = 0
- var tooLong = 0
- var adapter_stats: mutable.Map[String, Int] = mutable.Map()
-
- for (json <- jsons) {
- affected += json.field("num_reads_affected").get.numberOrZero.toInt
- tooShort += json.field("num_reads_discarded_too_short").get.numberOrZero.toInt
- tooLong += json.field("num_reads_discarded_too_long").get.numberOrZero.toInt
-
- val adapters = json.fieldOrEmptyObject("adapters")
- for (key <- adapters.objectFieldsOrEmpty) {
- val number = adapters.field(key).get.numberOrZero.toInt
- if (adapter_stats.contains(key)) adapter_stats(key) += number
- else adapter_stats += (key -> number)
- }
- }
-
- return ("num_reads_affected" := affected) ->:
- ("num_reads_discarded_too_short" := tooShort) ->:
- ("num_reads_discarded_too_long" := tooLong) ->:
- ("adapters" := adapter_stats.toMap) ->:
- jEmptyObject
- }
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index c7554f0e4..cd9dd4ae0 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -23,11 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.Output
import scala.io.Source
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.utils.ConfigUtils
/**
* FastQC wrapper with added functionality for the Flexiprep pipeline
@@ -142,32 +138,6 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
} else Set()
}
- /**
- * Summary of the FastQC run, stored in a [[Json]] object
- *
- * @deprecated
- */
- def summary: Json = {
-
- val outputMap =
- Map("plot_duplication_levels" -> "Images/duplication_levels.png",
- "plot_kmer_profiles" -> "Images/kmer_profiles.png",
- "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
- "plot_per_base_n_content" -> "Images/per_base_n_content.png",
- "plot_per_base_quality" -> "Images/per_base_quality.png",
- "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
- "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
- "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
- "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
- "fastqc_data" -> "fastqc_data.txt")
- .map {
- case (name, relPath) =>
- name -> Map("path" -> (outputDir + File.separator + relPath))
- }
-
- ConfigUtils.mapToJson(outputMap)
- }
-
@Output
var outputFiles: List[File] = Nil
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 4199c69ec..785efc483 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -61,13 +61,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var fastqc_R1_after: Fastqc = _
var fastqc_R2_after: Fastqc = _
- //val summary = new FlexiprepSummary(this)
-
def init() {
require(outputDir != null, "Missing output directory on flexiprep module")
require(input_R1 != null, "Missing input R1 on flexiprep module")
- //require(sampleId != null, "Missing sample ID on flexiprep module")
- //require(libId != null, "Missing library ID on flexiprep module")
+ require(sampleId != null, "Missing sample ID on flexiprep module")
+ require(libId != null, "Missing library ID on flexiprep module")
paired = input_R2.isDefined
@@ -88,8 +86,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
case _ =>
}
-
- //summary.out = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".qc.summary.json")
}
def biopetScript() {
@@ -109,24 +105,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fastqc_R1 = Fastqc(this, input_R1, new File(outputDir, R1_name + ".fastqc/"))
add(fastqc_R1)
- //summary.addFastqc(fastqc_R1)
addSummarizable(fastqc_R1, "fastqc_R1")
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
- //val md5sum_R1 = Md5sum(this, input_R1, outputDir)
- //add(md5sum_R1)
- //summary.addMd5sum(md5sum_R1, R2 = false, after = false)
-
if (paired) {
fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
add(fastqc_R2)
addSummarizable(fastqc_R2, "fastqc_R2")
- //summary.addFastqc(fastqc_R2, R2 = true)
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
-
- //val md5sum_R2 = Md5sum(this, input_R2.get, outputDir)
- //add(md5sum_R2)
- //summary.addMd5sum(md5sum_R2, R2 = true, after = false)
}
}
@@ -165,14 +151,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
seqstat_R1.isIntermediate = true
add(seqstat_R1)
addSummarizable(seqstat_R1, "seqstat_R1")
- //summary.addSeqstat(seqstat_R1, R2 = false, after = false, chunk)
if (paired) {
val seqstat_R2 = Seqstat(this, R2, outDir)
seqstat_R2.isIntermediate = true
add(seqstat_R2)
addSummarizable(seqstat_R2, "seqstat_R2")
- //summary.addSeqstat(seqstat_R2, R2 = true, after = false, chunk)
}
if (!skipClip) { // Adapter clipping
@@ -182,7 +166,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
cutadapt_R1.isIntermediate = true
add(cutadapt_R1)
addSummarizable(cutadapt_R1, "clipping_R1")
- //summary.addCutadapt(cutadapt_R1, R2 = false, chunk)
R1 = cutadapt_R1.fastq_output
deps ::= R1
outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
@@ -194,7 +177,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
cutadapt_R2.isIntermediate = true
add(cutadapt_R2)
addSummarizable(cutadapt_R2, "clipping_R2")
- //summary.addCutadapt(cutadapt_R2, R2 = true, chunk)
R2 = cutadapt_R2.fastq_output
deps ::= R2
@@ -208,7 +190,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fqSync.deps :::= deps
add(fqSync)
addSummarizable(fqSync, "fastq_sync")
- //summary.addFastqcSync(fqSync, chunk)
outputFiles += ("syncStats" -> fqSync.outputStats)
R1 = fqSync.outputFastq1
R2 = fqSync.outputFastq2
@@ -230,7 +211,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
sickle.isIntermediate = true
add(sickle)
addSummarizable(sickle, "trimming")
- //summary.addSickle(sickle, chunk)
R1 = sickle.output_R1
if (paired) R2 = sickle.output_R2
}
@@ -238,13 +218,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val seqstat_R1_after = Seqstat(this, R1, outDir)
seqstat_R1_after.deps = deps
add(seqstat_R1_after)
- //summary.addSeqstat(seqstat_R1_after, R2 = false, after = true, chunk)
+ addSummarizable(seqstat_R1_after, "seqstat_R1_after")
if (paired) {
val seqstat_R2_after = Seqstat(this, R2, outDir)
seqstat_R2_after.deps = deps
add(seqstat_R2_after)
- //summary.addSeqstat(seqstat_R2_after, R2 = true, after = true, chunk)
+ addSummarizable(seqstat_R2_after, "seqstat_R2_after")
}
outputFiles += (chunk + "output_R1" -> R1)
@@ -264,27 +244,17 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (paired) outputFiles += ("output_R2_gzip" -> R2)
if (!skipTrim || !skipClip) {
- val md5sum_R1 = Md5sum(this, R1, outputDir)
- add(md5sum_R1)
- //summary.addMd5sum(md5sum_R1, R2 = false, after = true)
- if (paired) {
- val md5sum_R2 = Md5sum(this, R2, outputDir)
- add(md5sum_R2)
- //summary.addMd5sum(md5sum_R2, R2 = true, after = true)
- }
fastqc_R1_after = Fastqc(this, R1, new File(outputDir, R1_name + ".qc.fastqc/"))
add(fastqc_R1_after)
addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
- //summary.addFastqc(fastqc_R1_after, after = true)
+
if (paired) {
fastqc_R2_after = Fastqc(this, R2, new File(outputDir, R2_name + ".qc.fastqc/"))
add(fastqc_R2_after)
addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
- //summary.addFastqc(fastqc_R2_after, R2 = true, after = true)
}
}
- //add(summary)
addSummaryJobs
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
deleted file mode 100644
index 86a483166..000000000
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ /dev/null
@@ -1,242 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-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.{ Md5sum, Seqstat }
-import nl.lumc.sasc.biopet.tools.FastqSync
-import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
-class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Configurable {
- this.analysisName = getClass.getSimpleName
-
- @Input(doc = "deps")
- var deps: List[File] = Nil
-
- @Output(doc = "Summary output", required = true)
- var out: File = _
-
- class Chunk {
- var seqstatR1: Seqstat = _
- var seqstatR2: Seqstat = _
- var seqstatR1after: Seqstat = _
- var seqstatR2after: Seqstat = _
-
- var cutadaptR1: Cutadapt = _
- var cutadaptR2: Cutadapt = _
-
- var fastqSync: FastqSync = _
-
- var sickle: Sickle = _
- }
-
- var chunks: Map[String, Chunk] = Map()
-
- var md5R1: Md5sum = _
- var md5R2: Md5sum = _
- var md5R1after: Md5sum = _
- var md5R2after: Md5sum = _
-
- var fastqcR1: Fastqc = _
- var fastqcR2: Fastqc = _
- var fastqcR1after: Fastqc = _
- var fastqcR2after: Fastqc = _
-
- var flexiprep: Flexiprep = if (root.isInstanceOf[Flexiprep]) root.asInstanceOf[Flexiprep] else {
- throw new IllegalStateException("Root is no instance of Flexiprep")
- }
-
- var resources: Map[String, Json] = Map()
-
- def addFastqc(fastqc: Fastqc, R2: Boolean = false, after: Boolean = false): Fastqc = {
- if (!R2 && !after) this.fastqcR1 = fastqc
- else if (!R2 && after) this.fastqcR1after = fastqc
- else if (R2 && !after) this.fastqcR2 = fastqc
- else if (R2 && after) this.fastqcR2after = fastqc
- deps ::= fastqc.output
- return fastqc
- }
-
- def addMd5sum(md5sum: Md5sum, R2: Boolean = false, after: Boolean = false): Md5sum = {
- if (!R2 && !after) this.md5R1 = md5sum
- else if (!R2 && after) this.md5R1after = md5sum
- else if (R2 && !after) this.md5R2 = md5sum
- else if (R2 && after) this.md5R2after = md5sum
- deps ::= md5sum.output
- return md5sum
- }
-
- def addSeqstat(seqstat: Seqstat, R2: Boolean = false, after: Boolean = false, chunk: String = ""): Seqstat = {
- if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
- if (!R2 && !after) chunks(chunk).seqstatR1 = seqstat
- else if (!R2 && after) chunks(chunk).seqstatR1after = seqstat
- else if (R2 && !after) chunks(chunk).seqstatR2 = seqstat
- else if (R2 && after) chunks(chunk).seqstatR2after = seqstat
- deps ::= seqstat.output
- return seqstat
- }
-
- def addCutadapt(cutadapt: Cutadapt, R2: Boolean = false, chunk: String = ""): Cutadapt = {
- if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
- if (!R2) chunks(chunk).cutadaptR1 = cutadapt
- else chunks(chunk).cutadaptR2 = cutadapt
- deps ::= cutadapt.stats_output
- return cutadapt
- }
-
- def addSickle(sickle: Sickle, chunk: String = ""): Sickle = {
- if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
- chunks(chunk).sickle = sickle
- deps ::= sickle.output_stats
- return sickle
- }
-
- def addFastqcSync(fastqSync: FastqSync, chunk: String = ""): FastqSync = {
- if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
- chunks(chunk).fastqSync = fastqSync
- deps ::= fastqSync.outputStats
- fastqSync
- }
- // format: OFF
- override def run {
- logger.debug("Start")
- md5Summary()
- val summary =
- ("samples" := ( flexiprep.sampleId.getOrElse("x") :=
- ("libraries" := ( flexiprep.libId.getOrElse("x") := (
- ("flexiprep" := (
- ("clipping" := !flexiprep.skipClip) ->:
- ("trimming" := !flexiprep.skipTrim) ->:
- ("paired" := flexiprep.paired) ->:
- jEmptyObject)) ->:
- ("stats" := (
- ("fastq" := seqstatSummary) ->:
- ("clipping" :=? clipstatSummary) ->?:
- ("trimming" :=? trimstatSummary) ->?:
- jEmptyObject)) ->:
- ("resources" := (("raw_R1" := getResources(fastqcR1, md5R1)) ->:
- ("raw_R2" :?= getResources(fastqcR2, md5R2)) ->?:
- ("proc_R1" :?= getResources(fastqcR1after, md5R1after)) ->?:
- ("proc_R2" :?= getResources(fastqcR2after, md5R2after)) ->?:
- jEmptyObject)) ->:
- jEmptyObject ))->: jEmptyObject)->: jEmptyObject)->: jEmptyObject) ->: jEmptyObject
- // format: ON
- 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_chunks = for ((key, value) <- chunks) yield value.seqstatR1.getSummary
- val R1: Json = Seqstat.mergeSummaries(R1_chunks.toList)
-
- val R2: Option[Json] = if (!flexiprep.paired) None
- else if (chunks.size == 1) Option(chunks.head._2.seqstatR2.getSummary)
- else {
- val s = for ((key, value) <- chunks) yield value.seqstatR2.getSummary
- Option(Seqstat.mergeSummaries(s.toList))
- }
- val R1_proc: Option[Json] = if (flexiprep.skipClip && flexiprep.skipTrim) None
- else if (chunks.size == 1) Option(chunks.head._2.seqstatR1after.getSummary)
- else {
- val s = for ((key, value) <- chunks) yield value.seqstatR1after.getSummary
- Option(Seqstat.mergeSummaries(s.toList))
- }
- val R2_proc: Option[Json] = if (!flexiprep.paired || (flexiprep.skipClip && flexiprep.skipTrim)) None
- else if (chunks.size == 1) Option(chunks.head._2.seqstatR2after.getSummary)
- else {
- val s = for ((key, value) <- chunks) yield value.seqstatR2after.getSummary
- Option(Seqstat.mergeSummaries(s.toList))
- }
- return Option(("R1_raw" := R1) ->:
- ("R2_raw" :=? R2) ->?:
- ("R1_proc" :=? R1_proc) ->?:
- ("R2_proc" :=? R2_proc) ->?:
- jEmptyObject)
- }
-
- def md5Summary() {
- val R1_raw = md5Summary(md5R1)
- val R2_raw = md5Summary(md5R2)
- val R1_proc = md5Summary(md5R1after)
- val R2_proc = md5Summary(md5R2after)
-
- if (!R1_raw.isEmpty) resources += ("fastq_R1_raw" -> R1_raw.get)
- if (!R2_raw.isEmpty) resources += ("fastq_R2_raw" -> R2_raw.get)
- if (!R1_proc.isEmpty) resources += ("fastq_R1_proc" -> R1_proc.get)
- if (!R2_proc.isEmpty) resources += ("fastq_R2_proc" -> R2_proc.get)
- }
-
- def md5Summary(md5sum: Md5sum): Option[Json] = {
- if (md5sum == null) return None
- else return Option(md5sum.getSummary)
- }
-
- def getResources(fastqc: Fastqc, md5sum: Md5sum): Option[Json] = {
- if (fastqc == null || md5sum == null) return None
- val fastqcSum = fastqcSummary(fastqc).get
- return Option(("fastq" := md5Summary(md5sum)) ->: fastqcSum)
- }
-
- def fastqcSummary(fastqc: Fastqc): Option[Json] = {
- if (fastqc == null) return None
- else return Option(fastqc.summary)
- }
-
- def clipstatSummary(): Option[Json] = {
- if (flexiprep.skipClip) return None
- val R1: Json = if (chunks.size == 1) chunks.head._2.cutadaptR1.getSummary
- else {
- val s = for ((key, value) <- chunks) yield value.cutadaptR1.getSummary
- Cutadapt.mergeSummaries(s.toList)
- }
- val R2: Option[Json] = if (!flexiprep.paired) None
- else if (chunks.size == 1) Option(chunks.head._2.cutadaptR2.getSummary)
- else {
- val s = for ((key, value) <- chunks) yield value.cutadaptR2.getSummary
- Option(Cutadapt.mergeSummaries(s.toList))
- }
- return Option(("R1" := R1) ->:
- ("R2" :=? R2) ->?:
- ("fastq_sync" :=? syncstatSummary) ->?:
- jEmptyObject)
- }
-
- def syncstatSummary(): Option[Json] =
- if (flexiprep.skipClip || !flexiprep.paired)
- None
- else {
- val s = for ((key, value) <- chunks) yield value.fastqSync.summary
- Option(FastqSync.mergeSummaries(s.toList))
- }
-
- def trimstatSummary(): Option[Json] = {
- if (flexiprep.skipTrim) return None
- if (chunks.size == 1) return Option(chunks.head._2.sickle.getSummary)
- else {
- val s = for ((key, value) <- chunks) yield value.sickle.getSummary
- return Option(Sickle.mergeSummaries(s.toList))
- }
- }
-}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
index 0ec269874..dc63f70bf 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
@@ -66,51 +66,4 @@ class Sickle(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Sickle(r
Map("input_R1" -> input_R1, "output_R1" -> output_R1) ++
(if (input_R2 != null) Map("input_R2" -> input_R2, "output_R2" -> output_R2) else Map())
}
-
- def getSummary: Json = {
- val pairKept = """FastQ paired records kept: (\d*) \((\d*) pairs\)""".r
- val singleKept = """FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
- val pairDiscarded = """FastQ paired records discarded: (\d*) \((\d*) pairs\)""".r
- val singleDiscarded = """FastQ single records discarded: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
-
- var stats: mutable.Map[String, Int] = mutable.Map()
-
- if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
- line match {
- case pairKept(reads, pairs) => stats += ("num_paired_reads_kept" -> reads.toInt)
- case singleKept(total, r1, r2) => {
- stats += ("num_reads_kept_R1" -> r1.toInt)
- stats += ("num_reads_kept_R2" -> r2.toInt)
- }
- case pairDiscarded(reads, pairs) => stats += ("num_paired_reads_discarded" -> reads.toInt)
- case singleDiscarded(total, r1, r2) => {
- stats += ("num_reads_discarded_R1" -> r1.toInt)
- stats += ("num_reads_discarded_R2" -> r2.toInt)
- }
- case _ =>
- }
- }
-
- val temp = ("" := stats.toMap) ->: jEmptyObject
- return temp.fieldOrEmptyObject("")
- }
}
-
-object Sickle {
- def mergeSummaries(jsons: List[Json]): Json = {
- var total: mutable.Map[String, Int] = mutable.Map()
-
- for (json <- jsons) {
- for (key <- json.objectFieldsOrEmpty) {
- if (json.field(key).get.isNumber) {
- val number = json.field(key).get.numberOrZero.toInt
- if (total.contains(key)) total(key) += number
- else total += (key -> number)
- }
- }
- }
-
- val temp = ("" := total.toMap) ->: jEmptyObject
- return temp.fieldOrEmptyObject("")
- }
-}
\ No newline at end of file
--
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