From 68b01fdc371823840539bc51bd2ebf686409d8ba Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 23 Aug 2015 13:49:46 +0200
Subject: [PATCH] Added UCSC header skipping
---
.../biopet/utils/intervals/BedRecord.scala | 2 +-
.../utils/intervals/BedRecordList.scala | 37 ++++++++++++-------
2 files changed, 24 insertions(+), 15 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
index c395d0bc5..9a798fbaf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
@@ -81,7 +81,7 @@ case class BedRecord(chr: String,
object BedRecord {
def fromLine(line: String): BedRecord = {
val values = line.split("\t")
- require(values.length >= 3)
+ require(values.length >= 3, "Not enough columns count for a bed file")
BedRecord(
values(0),
values(1).toInt,
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index 783f32481..029356e5f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
@@ -10,7 +10,7 @@ import nl.lumc.sasc.biopet.core.Logging
/**
* Created by pjvan_thof on 8/20/15.
*/
-class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
+class BedRecordList(val chrRecords: Map[String, List[BedRecord]], header: List[String] = Nil) {
def allRecords = for (chr <- chrRecords; record <- chr._2) yield record
lazy val sort = {
@@ -58,29 +58,38 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
}
object BedRecordList {
- def fromList(records: Traversable[BedRecord]): BedRecordList = fromList(records.toIterator)
+ def fromListWithHeader(records: Traversable[BedRecord],
+ header: List[String]): BedRecordList = fromListWithHeader(records.toIterator, header)
- def fromList(records: TraversableOnce[BedRecord]): BedRecordList = {
+ def fromListWithHeader(records: TraversableOnce[BedRecord], header: List[String]): BedRecordList = {
val map = mutable.Map[String, ListBuffer[BedRecord]]()
for (record <- records) {
if (!map.contains(record.chr)) map += record.chr -> ListBuffer()
map(record.chr) += record
}
- new BedRecordList(map.toMap.map(m => m._1 -> m._2.toList))
+ new BedRecordList(map.toMap.map(m => m._1 -> m._2.toList), header)
}
+ def fromList(records: Traversable[BedRecord]): BedRecordList = fromListWithHeader(records.toIterator, Nil)
+
+ def fromList(records: TraversableOnce[BedRecord]): BedRecordList = fromListWithHeader(records, Nil)
+
def fromFile(bedFile: File) = {
- var lineCount = 0L
- fromList(Source.fromFile(bedFile).getLines().map(line => {
- lineCount += 1
- try {
+ val reader = Source.fromFile(bedFile)
+ val all = reader.getLines().toList
+ val header = all.takeWhile(x => x.startsWith("browser") || x.startsWith("track"))
+ var lineCount = header.length
+ val content = all.drop(lineCount)
+ try {
+ fromListWithHeader(content.map(line => {
+ lineCount += 1
BedRecord.fromLine(line).validate
- } catch {
- case e: Exception =>
- Logging.logger.error(s"Parsing line number $lineCount failed on file: ${bedFile.getAbsolutePath}")
- throw e
- }
- }))
+ }), header)
+ } catch {
+ case e: Exception =>
+ Logging.logger.error(s"Parsing line number $lineCount failed on file: ${bedFile.getAbsolutePath}")
+ throw e
+ }
}
def combineOverlap(list: BedRecordList): BedRecordList = {
--
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