Hi Dave, BioJava does currently not allow to convert between different multiple sequence file formats , if that is what you want to do. We have had a few requests over time to be able to read a profile from some of the popular multiple sequence alignment file formats. I'll add it as a feature request on github.
Thanks, Andreas On Sun, Dec 21, 2014 at 11:09 PM, Michael Heuer <[email protected]> wrote: > Hello Dave, > > From what I can tell from the biojava3-alignment API > > http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html > > and the detailed notes from Mark Chapman's GSoC MSA project > > http://biojava.org/wiki/GSoC:MSA > > I don't think you can read in an existing MSA from a file into the > biojava3 Profile class. You could just perform the MSA with biojava3 > > http://biojava.org/wiki/BioJava:CookBook3:MSA > > > Alternatively, in biojava-legacy there is a clustalw parser > > > http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html > > I've never used that package though and don't know how well it has kept up > with changes to clustalw if at all. > > michael > > > > > On Sat, Dec 20, 2014 at 3:41 PM, Dave Roe <[email protected]> wrote: > >> I can't figure out how to create a Profile object from a MSA file (e.g., >> .msf) in biojava3. Any suggestions? >> -- >> Dave >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://mailman.open-bio.org/mailman/listinfo/biojava-l >> > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic RCSB PDB Protein Data Bank University of California, San Diego Editor Software Section PLOS Computational Biology BioJava Project Lead -----------------------------------------------------------------------
_______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l
