Commit 9b465609 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change logging to logger.info

parent a32bc102
......@@ -73,7 +73,7 @@ object SageCountFastq extends ToolCommand {
if (counts.contains(seq)) counts(seq) += 1
else counts += (seq -> 1)
count += 1
if (count % 1000000 == 0) System.err.println(count + " sequences done")
if (count % 1000000 == 0) logger.info(count + " sequences done")
}
})
logger.info(count + " sequences done")
......
......@@ -117,21 +117,21 @@ object SageCreateLibrary extends ToolCommand {
tagRegex = (commandArgs.tag + "[CATG]{" + commandArgs.length + "}").r
var count = 0
System.err.println("Reading fasta file")
logger.info("Reading fasta file")
val reader = FastaReaderHelper.readFastaDNASequence(commandArgs.input)
System.err.println("Finding tags")
logger.info("Finding tags")
for ((name, seq) <- reader) {
val result = getTags(name, seq, tagRegex)
addTagresultToTaglib(name, result)
count += 1
if (count % 10000 == 0) System.err.println(count + " transcripts done")
if (count % 10000 == 0) logger.info(count + " transcripts done")
}
System.err.println(count + " transcripts done")
logger.info(count + " transcripts done")
System.err.println("Start sorting tags")
logger.info("Start sorting tags")
val tagGenesMapSorted: SortedMap[String, TagGenes] = SortedMap(tagGenesMap.toArray: _*)
System.err.println("Writting output files")
logger.info("Writting output files")
val writer = new PrintWriter(commandArgs.output)
writer.println("#tag\tfirstTag\tAllTags\tFirstAntiTag\tAllAntiTags")
for ((tag, genes) <- tagGenesMapSorted) {
......
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