Henk, That worked perfectly. I would have never guessed.
Thanks, Jason Flowers Henk C. den Bakker wrote: > Hi Jason, > > I had the same problem, it turns out that the JGI genbank files have > 'empty' accession and version values. Once you fill in these values > they are properly recognized by Mauve. > > Here is an example: > > original JGI genbank file: > > LOCUS Chromosome 3118565 bp DNA linear > 10-JUL-2009 > DEFINITION chromosome Chromosome. > ACCESSION VERSION KEYWORDS . > > change this into something like: > > LOCUS Chromosome 3118565 bp DNA linear > 10-JUL-2009 > DEFINITION chromosome Chromosome. > ACCESSION tralalai2 > VERSION tralalai2.1 > KEYWORDS . > > and it works perfectly fine in Mauve > > I hope this works for you, > > Best > Henk > > Jason Flowers wrote: >> Sorry for sending another message since this has been so active >> recently, but I have a genome genbank file that I downloaded from JGI >> that does not display the annotation in the alignment view. The file >> is readable by artemis and shows all of the annotation, so I assume >> that it is in the correct format. I have been able to view the >> annotations from other genomes that I downloaded from JGI, so I am >> not sure what the problem is. Below is the error message that I >> get. Any suggestions on what is wrong would be appreciated. >> >> Sincerely, >> >> Jason Flowers >> >> >> >> Error reading file. >> >> org.biojava.bio.BioException: Could not read sequence >> >> at >> org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:108) >> >> at >> org.gel.mauve.format.BaseFormat$2.nextSequence(BaseFormat.java:113) >> >> at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:175) >> >> at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:105) >> >> at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:59) >> >> at org.gel.mauve.XmfaViewerModel.init(XmfaViewerModel.java:151) >> >> at org.gel.mauve.XmfaViewerModel.<init>(XmfaViewerModel.java:43) >> >> at org.gel.mauve.ModelBuilder.buildModel(ModelBuilder.java:284) >> >> at org.gel.mauve.gui.FrameLoader.loadFile(FrameLoader.java:87) >> >> at org.gel.mauve.gui.FrameLoader.run(FrameLoader.java:57) >> >> at java.lang.Thread.run(Unknown Source) >> >> Caused by: java.lang.StringIndexOutOfBoundsException: String index >> out of range: 12 >> >> at java.lang.String.substring(Unknown Source) >> >> at >> org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankContext.java:308) >> >> >> >> at >> org.biojava.bio.seq.io.GenbankContext.processLine(GenbankContext.java:129) >> >> >> at >> org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:146) >> >> >> at >> org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105) >> >> ... 10 more >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> From must be less than To: /function=" >> >> >> Any advice would be appreciated >> >> ------------------------------------------------------------------------------ >> >> >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and >> stay ahead of the curve. Join us from November 9 - 12, 2009. Register >> now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Mauve-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/mauve-users >> >> > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
