Re: The root node is missing when parsing nexus tree files from MrBayes
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hi, Tiago, I found a mail from 2009/11/16 which says that your patch got committed. Is this the one you are referring to? Martin, this would mean that the patch is available through the biojava-legacy project (biojava v. 1.8) Andreas 2011/1/25 Tiago Antão <[email protected]>: > I think the patch that I submitted to the old newick module of biojava > never really was released by the biojava team. So that example will > not work with biojava (unless you track the svn release with the patch > and use that, arguably not a good solution). > > More info can be supplied by the biojava maintainers. I just made the > patch and the example. > > On Tue, Jan 25, 2011 at 5:35 PM, Martin Jones <[email protected]> wrote: >> Hi, >> >> I am using some of the code from here: >> >> http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/ >> >> to parse nexus phylogenetic tree data. My nexus file is output from MrBayes: >> >> ------------------ snip----------------- >> #NEXUS >> >> [ID: 7166567671] >> begin trees; >> [Note: This tree contains information on the topology, >> branch lengths (if present), and the probability >> of the partition indicated by the branch.] >> tree con_50_majrule = >> (27563:0.194008,(6843:0.233188,6960:0.229043)0.98:0.117649,(61985:0.217735,6657:0.275071)0.89:0.089314); >> >> [Note: This tree contains information only on the topology >> and branch lengths (mean of the posterior probability density).] >> tree con_50_majrule = >> (27563:0.194008,(6843:0.233188,6960:0.229043):0.117649,(61985:0.217735,6657:0.275071):0.089314); >> end; >> >> -------------------------- snip ------------- >> >> the file parses without any error, but when I get a list of vertices, >> the first one (27563) is missing: >> >> def tree = getTree(nexus, 'con 50 majrule') >> tree.vertexSet().each{ >> println it >> } >> >> output: >> >> 6843 >> p1 >> 6960 >> 61985 >> p3 >> 6657 >> p2 >> >> ______________snip ___________ >> >> The above code is Groovy, but hopefully is self-explanatory. Is the >> first node being treated specially because it is the root? If so, can >> I get it using some other method? >> >> Thanks, >> >> Martin >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -- > "If you want to get laid, go to college. If you want an education, go > to the library." - Frank Zappa > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l