Changeset 5770

Timestamp:

Dec 3, 2019, 9:40:36 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1208: Implement wizard for building database of variant frequencies in SCAN-B samples

Progress reporting is now supported by the python script.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantStatisticsJobCreator.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantStatisticsJobCreator.java

@@ -123 +123 @@
     String statCmd = "./mut_stats.py";
     statCmd += " ${WD}/vcflist.txt";
+    statCmd += " ${WD}/progress";
     statCmd += " > mut_stats.vcf";
     script.cmd(statCmd);
@@ -155 +156 @@
     int total = alignments.size();
     Pattern specimenName = Pattern.compile("(\\d+\\.\\d+)\\..*"); // Extract specimen name by taking first part of alignment name
+
     for (DerivedBioAssay alignment : alignments)
     {
@@ -179 +181 @@
       String patient = patients.get(0).getName();
       String dataFolder = ScriptUtil.checkValidPath((String)Annotationtype.DATA_FILES_FOLDER.getAnnotationValue(dc, manager, alignment), true, true);
-      tw.tablePrintData(patient, projectRoot + dataFolder+"/variants-raw.vcf.gz");
+      tw.tablePrintData(patient, projectRoot+dataFolder+"/variants-raw.vcf.gz", alignment.getName());
     }
     tw.flush();