From 3049d5721f38bd322fcdcb12765a197121c3551a Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 19 Jan 2016 11:51:19 +0100
Subject: [PATCH] Update Cutadapt wrapper and style change (camelCaps instead
of _)
---
.../sasc/biopet/extensions/Cutadapt.scala | 75 +++++++++----------
.../biopet/pipelines/flexiprep/Cutadapt.scala | 6 +-
.../pipelines/flexiprep/QcCommand.scala | 16 ++--
3 files changed, 48 insertions(+), 49 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index 3f57f9408..91037fa4e 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -26,19 +26,19 @@ import scala.collection.mutable
import scala.io.Source
/**
- * Extension for cutadapt
- * Started with version 1.5
- * Updated to version 1.9 (18-01-2016 by wyleung)
- * */
+ * Extension for cutadapt
+ * Started with version 1.5
+ * Updated to version 1.9 (18-01-2016 by wyleung)
+ */
class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
@Input(doc = "Input fastq file")
- var fastq_input: File = _
+ var fastqInput: File = _
@Output
- var fastq_output: File = _
+ var fastqOutput: File = _
@Output(doc = "Output statistics file")
- var stats_output: File = _
+ var statsOutput: File = _
executable = config("exe", default = "cutadapt")
def versionCommand = executable + " --version"
@@ -47,10 +47,10 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
/** Name of the key containing clipped adapters information in the summary stats. */
def adaptersStatsName = "adapters"
- var default_clip_mode: String = config("default_clip_mode", default = "3")
- var opt_adapter: Set[String] = config("adapter", default = Nil)
- var opt_anywhere: Set[String] = config("anywhere", default = Nil)
- var opt_front: Set[String] = config("front", default = Nil)
+ var defaultClipMode: String = config("default_clip_mode", default = "3")
+ var adapter: Set[String] = config("adapter", default = Nil)
+ var anywhere: Set[String] = config("anywhere", default = Nil)
+ var front: Set[String] = config("front", default = Nil)
var errorRate: Option[Double] = config("error_rate")
var noIndels: Boolean = config("no_indels", default = false)
@@ -60,17 +60,17 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
var noMatchAdapterWildcards: Boolean = config("no_match_adapter_wildcards", default = false) // specific for 1.9
/** Options for filtering of processed reads */
- var opt_discard: Boolean = config("discard", default = false)
- var trimmed_only: Boolean = config("trimmed_only", default = false)
- var opt_minimum_length: Int = config("minimum_length", 1)
- var opt_maximum_length: Option[Int] = config("maximum_length")
+ var discard: Boolean = config("discard", default = false)
+ var trimmedOnly: Boolean = config("trimmed_only", default = false)
+ var minimumLength: Int = config("minimum_length", 1)
+ var maximumLength: Option[Int] = config("maximum_length")
var noTrim: Boolean = config("no_trim", default = false)
var maxN: Option[Int] = config("max_n") // specific for 1.9
var maskAdapter: Boolean = config("mask_adapter", default = false)
/** Options that influence what gets output to where */
var quiet: Boolean = config("quiet", default = false)
-// var output: File // see up @Output
+ // var output: File // see up @Output
var infoFile: Option[File] = config("info_file")
var restFile: Option[File] = config("rest_file")
var wildcardFile: Option[File] = config("wildcard_file")
@@ -89,31 +89,30 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
var lengthTag: Option[String] = config("length_tag")
/** Colorspace options */
- var colorspace: Boolean = config("colorspace", default=false)
- var doubleEncode: Boolean = config("double_encode", default=false)
- var trimPrimer: Boolean = config("trim_primer", default=false)
- var stripF3: Boolean = config("strip_f3", default=false)
- var maq: Boolean = config("maq", default=false)
- var bwa: Boolean = config("bwa", default=false)
- var noZeroCap: Boolean = config("no_zero_cap", default= false)
- var zeroCap: Boolean = config("zero_cap", default=false)
+ var colorspace: Boolean = config("colorspace", default = false)
+ var doubleEncode: Boolean = config("double_encode", default = false)
+ var trimPrimer: Boolean = config("trim_primer", default = false)
+ var stripF3: Boolean = config("strip_f3", default = false)
+ var maq: Boolean = config("maq", default = false)
+ var bwa: Boolean = config("bwa", default = false)
+ var noZeroCap: Boolean = config("no_zero_cap", default = false)
+ var zeroCap: Boolean = config("zero_cap", default = false)
/** Paired end options */
var peAdapter: Set[String] = config("pe_adapter", default = Nil)
var peAdapterFront: Set[String] = config("pe_adapter_front", default = Nil)
var peAdapterBoth: Set[String] = config("pe_adapter_both", default = Nil)
- var peCut: Boolean = config("pe_cut", default=false)
+ var peCut: Boolean = config("pe_cut", default = false)
var pairedOutput: Option[File] = config("paired_output")
- var interleaved: Boolean = config("interleaved", default=false)
+ var interleaved: Boolean = config("interleaved", default = false)
var untrimmedPairedOutput: Option[File] = config("untrimmed_paired_output")
-
/** return commandline to execute */
def cmdLine = required(executable) +
// Options that influence how the adapters are found
- repeat("-a", opt_adapter) +
- repeat("-b", opt_anywhere) +
- repeat("-g", opt_front) +
+ repeat("-a", adapter) +
+ repeat("-b", anywhere) +
+ repeat("-g", front) +
optional("--error-rate", errorRate) +
conditional(noIndels, "--no-indels") +
optional("--times", times) +
@@ -121,10 +120,10 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
conditional(matchReadWildcards, "--match-read-wildcards") +
conditional(noMatchAdapterWildcards, "--no-match-adapter-wildcards") +
// Options for filtering of processed reads
- conditional(opt_discard, "--discard") +
- conditional(trimmed_only, "--trimmed-only") +
- optional("-m", opt_minimum_length) +
- optional("-M", opt_maximum_length) +
+ conditional(discard, "--discard") +
+ conditional(trimmedOnly, "--trimmed-only") +
+ optional("-m", minimumLength) +
+ optional("-M", maximumLength) +
conditional(noTrim, "--no-trim") +
optional("--max-n", maxN) +
conditional(maskAdapter, "--mask-adapter") +
@@ -160,9 +159,9 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
optional("--paired-output", pairedOutput) +
optional("--untrimmed-paired-output", untrimmedPairedOutput) +
// input / output
- required(fastq_input) +
- (if (outputAsStsout) "" else required("--output", fastq_output) +
- " > " + required(stats_output))
+ required(fastqInput) +
+ (if (outputAsStsout) "" else required("--output", fastqOutput) +
+ " > " + required(statsOutput))
/** Output summary stats */
def summaryStats: Map[String, Any] = {
@@ -174,7 +173,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
val stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
val adapter_stats: mutable.Map[String, Int] = mutable.Map()
- if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines()) {
+ if (statsOutput.exists) for (line <- Source.fromFile(statsOutput).getLines()) {
line match {
case trimR(m) => stats += ("trimmed" -> m.toInt)
case tooShortR(m) => stats += ("tooshort" -> m.toInt)
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 b34b37722..f974f8c9a 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
@@ -46,16 +46,16 @@ class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.e
// adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
// sequences come from FastQC
case _ =>
- throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastq_input'.")
+ throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastqInput'.")
}
// FastQC found no adapters
case otherwise =>
;
- logger.debug(s"No adapters found for summarizing in '$fastq_input'.")
+ logger.debug(s"No adapters found for summarizing in '$fastqInput'.")
None
}
// "adapters" key not found ~ something went wrong in our part
- case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastq_input'.")
+ case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastqInput'.")
}
initStats.updated(adaptersStatsName, adapterCounts)
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
index 22a9a4a52..390d68b58 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -102,12 +102,12 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val foundAdapters = fastqc.foundAdapters.map(_.seq)
if (foundAdapters.nonEmpty) {
val cutadapt = new Cutadapt(root, fastqc)
- cutadapt.fastq_input = seqtk.output
- cutadapt.fastq_output = new File(output.getParentFile, input.getName + ".cutadapt.fq")
- cutadapt.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
- if (cutadapt.default_clip_mode == "3") cutadapt.opt_adapter ++= foundAdapters
- else if (cutadapt.default_clip_mode == "5") cutadapt.opt_front ++= foundAdapters
- else if (cutadapt.default_clip_mode == "both") cutadapt.opt_anywhere ++= foundAdapters
+ cutadapt.fastqInput = seqtk.output
+ cutadapt.fastqOutput = new File(output.getParentFile, input.getName + ".cutadapt.fq")
+ cutadapt.statsOutput = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
+ if (cutadapt.defaultClipMode == "3") cutadapt.adapter ++= foundAdapters
+ else if (cutadapt.defaultClipMode == "5") cutadapt.front ++= foundAdapters
+ else if (cutadapt.defaultClipMode == "both") cutadapt.anywhere ++= foundAdapters
addPipeJob(cutadapt)
Some(cutadapt)
} else None
@@ -117,7 +117,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val sickle = new Sickle(root)
sickle.output_stats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
sickle.input_R1 = clip match {
- case Some(c) => c.fastq_output
+ case Some(c) => c.fastqOutput
case _ => seqtk.output
}
sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
@@ -127,7 +127,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val outputFile = (clip, trim) match {
case (_, Some(t)) => t.output_R1
- case (Some(c), _) => c.fastq_output
+ case (Some(c), _) => c.fastqOutput
case _ => seqtk.output
}
--
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