Yes, in fact, the aligner uses a c++ parser that can interpret DNAstar format files. The graphical interface on the other hand, uses BioJava to parse sequence and annotation data. BioJava doesn't provide parsers for DNAstar .seq format files. I realize the DNAstar .seq and the GenBank format are similar in many regards, and it might even be possible to parse a DNAstar .seq using the existing BioJava GenBank parser. You could try this with Mauve by simply renaming a .seq file to have a .gbk file name extension, and doing a search and replace in the alignment XMFA to change the corresponding file names.
If that doesn't work, then I'm afraid you're out of luck until someone implements DNAstar file parsing in BioJava. If that comes to pass I'll be happy to update Mauve to use that version of BioJava. Cheers, -Aaron On Mon, 2010-07-26 at 16:10 -0500, Guy Plunkett III wrote: > Aaron, > > I was in a hurry and ran Mauve with some DNASTAR format .seq files without > converting them to .fas or .gbk first. The alignment seems to have run fine, > so the files were correctly recognized, but the display did not load. Here is > part of the console log: > > OS name is: Windows 7 arch: amd64 > Executing: > win64\progressiveMauve > --output=C:\Users\plunkettg\Documents\Assemblies\RS218\testing > --output-guide-tree=C:\Users\plunkettg\Documents\Assemblies\RS218\testing.guide_tree > > --backbone-output=C:\Users\plunkettg\Documents\Assemblies\RS218\testing.backbone > C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq > C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq > Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\raw6EBA.tmp > Sequence loaded successfully. > C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq 10138 base > pairs. > Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\raw6EE9.tmp > Sequence loaded successfully. > C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq > 5089232 base pairs. > > ... [omitted for brevity] ... > > done. > root alignment has 1 superintervals > root alignment length: 5089232 > Organisms have 50.6% GC > Completed without error. > Exception in thread "Thread-8" java.lang.RuntimeException: Unexpected format: > DNAstar > at > org.gel.mauve.format.SupportedFormatFactory.formatNameToFormat(Unknown Source) > at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) > at org.gel.mauve.XmfaViewerModel.init(Unknown Source) > at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source) > at org.gel.mauve.ModelBuilder.buildModel(Unknown Source) > at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source) > at org.gel.mauve.gui.FrameLoader.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > > If I try loading the alignment file, I get the last part of the above (from > Exception in thread). The actual alignment file notes that the files are in > the DNAstar format: > > #FormatVersion Mauve1 > #Sequence1File > C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq > #Sequence1Format DNAstar > #Annotation1File > C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq > #Annotation1Format DNAstar > #Sequence2File > C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq > #Sequence2Format DNAstar > #Annotation2File > C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq > #Annotation2Format DNAstar > #BackboneFile C:\Users\plunkettg\Documents\Assemblies\RS218\testing.bbcols > > 1:1-10138 + C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq > > ==== > > So my question is, if the alignment engine can recognize and deal with > DNASTAR format sequences, how hard would it be to have the display engine > read them as well? > > Partial disclaimer: I do work for DNASTAR now, but this question is not for > them. > > Cheers, > Guy > > > Dr. Guy Plunkett III > > Senior Scientist, Laboratory of Genetics & Genome Center, UW-Madison > Senior Scientist, DNASTAR > > Laboratory of Genetics, University of Wisconsin DNASTAR, Inc. > 425G Henry Mall Rm 5428 3801 Regent Street > Madison, WI 53706-1580 Madison, WI 53705 > (608) 890-0189 phone (608) 237-3081 phone > (608) 262-2976 fax (608) 258-7439 fax > g...@genome.wisc.edu plunke...@dnastar.com > > web: http://www.genome.wisc.edu/information/gplunkett.html > > > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://ad.doubleclick.net/clk;226879339;13503038;l? > http://clk.atdmt.com/CRS/go/247765532/direct/01/ > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
