Thanks Nicklas, that sounds like a good solution. Matt
On 2/7/08 08:09, "Nicklas Nordborg" <[EMAIL PROTECTED]> wrote: > Matthew Eldridge wrote: >> Hi, >> >> I¹ve been loading some Illumina Bead Summary (IBS) data into Base 2.7.0 >> using the illumina-plugins-1.1 package and got the following error when >> it tries to match up the Illumina ID, or Illumicode, with a >> corresponding feature ID read from the Illumina-supplied BGX annotation >> file. >> >> net.sf.basedb.core.BaseException: Item not found: Feature[Feature >> ID=0004280546] doesn't exist on array design when inserting spot 0004280546 >> at >> net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummary >> Importer.java:611) >> at >> net.sf.basedb.illumina.plugins.BeadSummaryImporter.run(BeadSummaryImporter.ja >> va:225) >> at >> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java: >> 108) >> at >> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:505) >> at java.lang.Thread.run(Thread.java:619) >> Caused by: net.sf.basedb.core.ItemNotFoundException: Item not found: >> Feature[Feature ID=0004280546] doesn't exist on array design >> at net.sf.basedb.core.RawDataBatcher.doInsert(RawDataBatcher.java:581) >> at net.sf.basedb.core.RawDataBatcher.insert(RawDataBatcher.java:525) >> at >> net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummary >> Importer.java:589) >> ... 4 more >> >> The BeadSummaryImporter class is left-padding with zeros the Illumina >> ID, presumably because in most BGX files the Array_Address_ID values are >> left-padded in this way and read into Base2 as such. However, for the >> BGX file I downloaded from Illumina¹s web site, >> MouseWG-6_V1_1_R3_11234304_A.bgx, the IDs are not padded hence the error >> message. From what I can tell, this appears to be an isolated case >> affecting just the MouseWG-6_V1_1_R[0-3]_11234304.bgx files. > > Somehow, this is not surprising... Illumina file formats has a history > of being unstable. Thanks for reporting this to us. > >> As a quick and dirty fix, I edited BeadSummaryImporter.java and removed >> the MD5.leftPad function call in importScandata, rebuilt the plugin and >> redeployed and that worked. > > I guess that after this "fix" the plug-in only works with that file and > not with the others that have the 0-padding. > >> But I thought I should alert the plugin >> developers to a potential inconsistency in the Illumina annotation >> files. Perhaps an alternative approach might be to strip zeros from >> Illumina feature IDs when read in from the BGX file? > > This will not work, since it would cause already imported data that has > the 0-padding to be unusable. The only possible solution I can see is to > let the BGX-importer do the 0-padding of Array_Address_ID values if this > is missing in the first place. > > I have added this as a ticket: http://baseplugins.thep.lu.se/ticket/121 > > /Nicklas > > > ------------------------------------------------------------------------- > Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! > Studies have shown that voting for your favorite open source project, > along with a healthy diet, reduces your potential for chronic lameness > and boredom. Vote Now at http://www.sourceforge.net/community/cca08 > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
