Hi Jason, It's taken me a couple days to get to it, but I've written a little program that can read XMFA and write out MAF. It's called xmfa2maf and it will appear in the "other programs" links for your favorite OS on the mauve snapshots site in the next day or so.
Beware, however, that even though the output looks correct to my eyes based on the MAF documentation here: http://genome.ucsc.edu/FAQ/FAQformat.html#format5 I don't have a good way to check it. So if something seems wrong please let me know. Also, some of the fancier features of MAF are not currently used, such as the codes to indicate relationships of a block to the previous and following blocks in the file and basically anything related to UCSC browser-specific features. Use of xmfa2maf will require not just the input xmfa but also the sequence files aligned in the xmfa. The program will complain that it can't open the files if the sequence files aren't accessible at the path encoded in the first lines of the xmfa file. -Aaron On Mon, 2010-07-19 at 16:50 -0400, jason sahl wrote: > Hi everyone. Has anyone had any luck converting xmfa into other > multiple alignment formats, such as maf? I was trying to convert to > maf with genomicvis > (http://www.cs.wisc.edu/graphics/Wiki/GenomicsVis/ContinuingGenomicVis), but > the maf format doesn't appear to be correct. I also tried Bioperl, but the > maf writer isn't implemented. Any advice would be appreciated. > > > thanks, > Jason > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
