<div dir="ltr">Hi Dave,<div><br></div><div>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.</div><div><br></div><div>Thanks,</div><div><br></div><div>Andreas</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Dec 21, 2014 at 11:09 PM, Michael Heuer <span dir="ltr"><<a href="mailto:heuermh@gmail.com" target="_blank">heuermh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hello Dave,<br><br></div>From what I can tell from the biojava3-alignment API<br><br><a href="http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html" target="_blank">http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html</a><br><br>and the detailed notes from Mark Chapman's GSoC MSA project<br><br><a href="http://biojava.org/wiki/GSoC:MSA" target="_blank">http://biojava.org/wiki/GSoC:MSA</a><br><br>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<br><br><a href="http://biojava.org/wiki/BioJava:CookBook3:MSA" target="_blank">http://biojava.org/wiki/BioJava:CookBook3:MSA</a><br><br><br></div>Alternatively, in biojava-legacy there is a clustalw parser<br><br><a href="http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html" target="_blank">http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html</a><br><br></div>I've never used that package though and don't know how well it has kept up with changes to clustalw if at all.<br><br></div> michael<br><br><div><div><br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Sat, Dec 20, 2014 at 3:41 PM, Dave Roe <span dir="ltr"><<a href="mailto:daveroe25@gmail.com" target="_blank">daveroe25@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">I can't figure out how to create a Profile object from a MSA file (e.g., .msf) in biojava3. Any suggestions?<span><font color="#888888"><br clear="all"><div><div><div><div dir="ltr"><div>-- <br></div>Dave<br></div></div></div>
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