From 44731da1be682d6fa22725a3345d5cf94e16f9b6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Apr 2016 20:04:19 +0200
Subject: [PATCH] Added more args
---
.../core/BiopetCommandLineFunction.scala | 12 +++
.../lumc/sasc/biopet/extensions/Snptest.scala | 75 +++++++++++++++++--
2 files changed, 80 insertions(+), 7 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index a413c8bad..a7bdaf92f 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -165,6 +165,18 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
this
}
+ def multiArg(argName: String, values: Iterable[Any], groupSize: Int = 1, minGroups: Int = 0, maxGroups: Int = 0): String = {
+ if (values.size % groupSize != 0)
+ Logging.addError(s"Arg '${argName}' values: '${values}' does not fit to a groupSize of ${groupSize}")
+ val groups = values.size / groupSize
+ if (groups < minGroups)
+ Logging.addError(s"Args '${argName}' need atleast $minGroups with size $groupSize")
+ if (maxGroups > 0 && groups > maxGroups)
+ Logging.addError(s"Args '${argName}' may only have $maxGroups with size $groupSize")
+ if (values.nonEmpty) required(argName) + values.map(required(_)).mkString
+ else ""
+ }
+
@Output(required = false)
private[core] var stdoutFile: Option[File] = None
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
index d1948f5f1..62668f454 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
@@ -60,6 +60,41 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
var conditionOn: List[String] = config("condition_on")
+ var priorAdd: List[String] = config("prior_add", default = Nil)
+ var priorCov: List[String] = config("prior_cov", default = Nil)
+ var priorDom: List[String] = config("prior_dom", default = Nil)
+ var priorGen: List[String] = config("prior_gen", default = Nil)
+ var priorHet: List[String] = config("prior_het", default = Nil)
+ var priorRec: List[String] = config("prior_rec", default = Nil)
+ var tDf: Option[String] = config("t_df")
+ var tPrior: Boolean = config("t_prior", default = false)
+
+ var priorMqtQ: Option[String] = config("prior_mqt_Q")
+ var priorQtVb: Option[String] = config("prior_qt_V_b")
+ var priorQtVq: Option[String] = config("prior_qt_V_q")
+ var priorQtA: Option[String] = config("prior_qt_a")
+ var priorQtB: Option[String] = config("prior_qt_b")
+ var priorQtMeanB: Option[String] = config("prior_qt_mean_b")
+ var priorQtMeanQ: Option[String] = config("prior_qt_mean_q")
+
+ var meanBf: List[String] = config("mean_bf", default = Nil)
+
+ var analysisDescription: Option[String] = config("analysis_description")
+ var analysisName: Option[String] = config("analysis_name")
+ var chunk: Option[Int] = config("chunk")
+ var debug: Boolean = config("debug", default = false)
+ var hwe: Boolean = config("hwe", default = false)
+ var lowerSampleLimit: Option[Int] = config("lower_sample_limit")
+ var overlap: Boolean = config("overlap", default = false)
+ var printids: Boolean = config("printids", default = false)
+ var quantileNormalisePhenotypes: Boolean = config("quantile_normalise_phenotypes", default = false)
+ var range: List[String] = config("range", default = Nil)
+ var renorm: Boolean = config("renorm", default = false)
+ var snpid: List[String] = config("snpid", default = Nil)
+ var useRawCovariates: Boolean = config("use_raw_covariates")
+ var useRawPhenotypes: Boolean = config("use_raw_phenotypes")
+ var noClobber: Boolean = config("no_clobber", default = false)
+
executable = config("exe", default = "snptest")
def versionCommand: String = executable + " -help"
@@ -70,16 +105,11 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
require(inputGenotypes.length == inputSampleFiles.length)
}
- def multiArg(argName: String, values: Iterable[Any]): String = {
- if (values.nonEmpty) required(argName) + values.map(required(_)).mkString
- else ""
- }
-
def cmdLine: String = {
val data = inputGenotypes.zip(inputSampleFiles).flatMap(x => List(x._1, x._2))
required(executable) +
optional("-assume_chromosome", assumeChromosome) +
- multiArg("-data", data) +
+ multiArg("-data", data, groupSize = 2) +
optional("-genotype_field", genotypeField) +
optional("-genotype_probability_scale", genotypeProbabilityScale) +
optional("-haploid_genotype_coding", haploidGenotypeCoding) +
@@ -107,7 +137,38 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
multiArg("-cov_names", covNames) +
optional("-sex_column", sexColumn) +
optional("-stratify_on", stratifyOn) +
- multiArg("-condition_on", conditionOn)
+ multiArg("-condition_on", conditionOn) +
+ multiArg("-prior_add", priorAdd, groupSize = 4, maxGroups = 1) +
+ multiArg("-prior_cov", priorCov, groupSize = 2, maxGroups = 1) +
+ multiArg("-prior_dom", priorDom, groupSize = 4, maxGroups = 1) +
+ multiArg("-prior_gen", priorGen, groupSize = 6, maxGroups = 1) +
+ multiArg("-prior_het", priorHet, groupSize = 4, maxGroups = 1) +
+ multiArg("-prior_rec", priorRec, groupSize = 4, maxGroups = 1) +
+ optional("-t_df", tDf) +
+ conditional(tPrior, "-t_prior") +
+ optional("-prior_mqt_Q", priorMqtQ) +
+ optional("-prior_qt_V_b", priorQtVb) +
+ optional("-prior_qt_V_q", priorQtVq) +
+ optional("-prior_qt_a", priorQtA) +
+ optional("-prior_qt_b", priorQtB) +
+ optional("-prior_qt_mean_b", priorQtMeanB) +
+ optional("-prior_qt_mean_q", priorQtMeanQ) +
+ multiArg("-mean_bf", meanBf, groupSize = 2, maxGroups = 1) +
+ optional("-analysis_description", analysisDescription) +
+ optional("-analysis_name", analysisName) +
+ optional("-chunk", chunk) +
+ conditional(debug, "-debug") +
+ conditional(hwe, "-hwe") +
+ optional("-lower_sample_limit", lowerSampleLimit) +
+ conditional(overlap, "-overlap") +
+ conditional(printids, "-printids") +
+ conditional(quantileNormalisePhenotypes, "quantile_normalise_phenotypes") +
+ multiArg("-range", range, groupSize = 2) +
+ conditional(renorm, "-renorm") +
+ multiArg("-snpid", snpid) +
+ conditional(useRawCovariates, "-use_raw_covariates") +
+ conditional(useRawPhenotypes, "-use_raw_phenotypes") +
+ conditional(noClobber, "-no_clobber")
}
}
--
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