From b03177621ce6f8e0481e6be17f98f82b7c57f186 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 26 May 2014 17:32:48 +0200
Subject: [PATCH] Added default_clip_mode option
---
.../lumc/sasc/biopet/wrappers/Cutadapt.scala | 39 +++++++++++++++----
1 file changed, 31 insertions(+), 8 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
index 644326bef..0e2ea0174 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
@@ -11,6 +11,7 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
def this() = this(new Config(Map()))
analysisName = "cutadapt"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig("cutadapt"), globalConfig)
+ logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Cutadapt exe", required=false)
var cutadapt_exe: File = new File(config.getAsString("exe","/usr/local/bin/cutadapt"))
@@ -18,17 +19,22 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
@Input(doc="Fastq contams file", required=false) var contams_file: File = _
@Output(doc="Output fastq file") var fastq_output: File = _
+ var default_clip_mode = config.getAsString("default_clip_mode", "3")
var opt_adapter: Set[String] = config.getAsListOfStrings("adapter", Nil).to[Set]
var opt_anywhere: Set[String] = config.getAsListOfStrings("anywhere", Nil).to[Set]
var opt_front: Set[String] = config.getAsListOfStrings("front", Nil).to[Set]
var opt_discard: Boolean = config.getAsBoolean("discard",false)
var opt_minimum_length: String = config.getAsInt("minimum_length", 1).toString
- var opt_maximum_length: String = if (config.contains("maximum_length")) config.getAsInt("maximum_length").toString else null
+ var opt_maximum_length: String = config.getAsString("maximum_length", null)
- def commandLine = {
+ def init() {
this.addJobReportBinding("version", getVersion)
this.getContamsFromFile
+ }
+
+ def commandLine = {
+ init()
if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
required(cutadapt_exe) +
// options
@@ -53,7 +59,13 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
if (contams_file.exists()) {
for (line <- fromFile(contams_file).getLines) {
var s: String = line.substring(line.lastIndexOf("\t")+1, line.size)
- opt_adapter += s
+ if (default_clip_mode == "3") opt_adapter += s
+ else if (default_clip_mode == "5") opt_front += s
+ else if (default_clip_mode == "both") opt_anywhere += s
+ else {
+ opt_adapter += s
+ logger.warn("Option default_clip_mode should be '3', '5' or 'both', falling back to default: '3'")
+ }
logger.info("Adapter: " + s + " found in: " + fastq_input)
}
} else logger.warn("File : " + contams_file + " does not exist")
@@ -61,11 +73,22 @@ class Cutadapt(val globalConfig: Config) extends CommandLineFunction {
}
private var version: String = _
- def getVersion : String = {
- if (version == null) {
- val v: String = (cutadapt_exe + " --version").!!.replace("\n", "")
- if (!v.isEmpty) version = v
+ var versionCommand = cutadapt_exe + " --version"
+ var versionRegex = """(.*)"""
+ def getVersion: String = getVersion(versionCommand, versionRegex)
+ def getVersion(cmd:String, regex:String) : String = {
+ val REG = regex.r
+ if (cmd.! != 0) {
+ logger.warn("Version command: '" + cmd + "' give a none-zero exit code, version not found")
+ return "NA"
+ }
+ for (line <- cmd.!!.split("\n")) {
+ line match {
+ case REG(m) => return m
+ case _ =>
+ }
}
- return version
+ logger.warn("Version command: '" + cmd + "' give a exit code 0 but no version was found, executeble oke?")
+ return "NA"
}
}
\ No newline at end of file
--
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