From 9a2c81d56938f4f9c696b5e035811b63bde84663 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Mar 2015 13:24:14 +0100
Subject: [PATCH] added counter
---
.../sasc/biopet/tools/VEPNormalizer.scala | 57 +++++++++----------
1 file changed, 26 insertions(+), 31 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
index 54f39071f..646f8dead 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
@@ -126,13 +126,17 @@ object VEPNormalizer extends ToolCommand {
logger.info(s"""You have selected mode $mode""")
logger.info("Start processing records")
+ var counter = 0
for (record <- reader) {
mode match {
case "explode" => explodeTranscripts(record, newInfos, removeCsq).foreach(vc => writer.add(vc))
case "standard" => writer.add(standardTranscripts(record, newInfos, removeCsq))
case _ => throw new IllegalArgumentException("Something odd happened!")
}
+ counter += 1
+ if (counter % 100000 == 0) logger.info(counter + " variants processed")
}
+ logger.info("done: " + counter + " variants processed")
}
/**
@@ -184,51 +188,42 @@ object VEPNormalizer extends ToolCommand {
* @return An array with the new records
*/
def explodeTranscripts(record: VariantContext, csqInfos: Array[String], removeCsq: Boolean): Array[VariantContext] = {
- val csq = record.getAttributeAsString("CSQ", "unknown")
-
- val builder = {
- if (removeCsq) new VariantContextBuilder(record).rmAttribute("CSQ")
- else new VariantContextBuilder(record)
- }
-
- // atributes for each transcript (transcript)(csq field index)
- val arti = csq.
- stripPrefix("[").
- stripSuffix("]").
- split(",").map(_.split("""\|"""))
+ val arti = parseCsq(record)
for (transcript <- arti) yield {
(for (
- fieldId <- 0 until csqInfos.size if transcript.isDefinedAt(fieldId) && !transcript(fieldId).isEmpty
- ) yield csqInfos(fieldId) -> transcript(fieldId).trim)
+ fieldId <- 0 until csqInfos.size if transcript.isDefinedAt(fieldId);
+ value = transcript(fieldId).trim if value.nonEmpty
+ ) yield csqInfos(fieldId) -> value)
.filterNot(_._2.isEmpty)
- .foldLeft(builder)((builder, artibute) => builder.attribute(artibute._1, artibute._2))
+ .foldLeft(createBuilder(record, removeCsq))((builder, artibute) => builder.attribute(artibute._1, artibute._2))
.make()
}
}
def standardTranscripts(record: VariantContext, csqInfos: Array[String], removeCsq: Boolean): VariantContext = {
- val csq = record.getAttributeAsString("CSQ", "unknown")
+ val arti = parseCsq(record)
- val builder = {
- if (removeCsq) new VariantContextBuilder(record).rmAttribute("CSQ")
- else new VariantContextBuilder(record)
- }
+ (for (fieldId <- 0 until csqInfos.size) yield csqInfos(fieldId) -> {
+ for (
+ transcript <- arti if transcript.isDefinedAt(fieldId);
+ value = transcript(fieldId).trim if value.nonEmpty
+ ) yield value
+ }).filter(_._2.nonEmpty)
+ .foldLeft(createBuilder(record, removeCsq))((builder, attribute) => builder.attribute(attribute._1, attribute._2))
+ .make()
+ }
+
+ protected def createBuilder(record: VariantContext, removeCsq: Boolean) = {
+ if (removeCsq) new VariantContextBuilder(record).rmAttribute("CSQ")
+ else new VariantContextBuilder(record)
+ }
- // atributes for each transcript (transcript)(csq field index)
- val arti = csq.
+ protected def parseCsq(record: VariantContext) = {
+ record.getAttributeAsString("CSQ", "unknown").
stripPrefix("[").
stripSuffix("]").
split(",").map(_.split("""\|"""))
-
- (for (fieldId <- 0 until csqInfos.size) yield csqInfos(fieldId) -> {
- for (
- transcript <- arti if transcript.isDefinedAt(fieldId) && !transcript(fieldId).isEmpty
- ) yield transcript(fieldId).trim
- })
- .filterNot(_._2.isEmpty)
- .foldLeft(builder)((builder, artibute) => builder.attribute(artibute._1, artibute._2))
- .make()
}
case class Args(inputVCF: File = null,
--
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