[Bioperl-l] BioPerl and NHX tree

[aaron.j.mackey at gsk.com]

Instead of using TreeIO::newick to read the tree, use TreeIO::nhx -- that 
way, your tree's nodes are already NodeNHX's.  Instead of creating a new 
$nodenhx, you can use the $node variable directly from the tree ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 01/03/2008 09:29:09 AM:

> Dear all,
> 
> I am trying to convert a newick tree into an NHX tree, so I can add the 
> taxid tag for each leaf.
> 
> I am using the modules: Bio::TreeIO  & Bio::Tree::NodeNHX
> The idea is
> 1) to read the newick tree
> 2) get the leaf, and get the corresponding taxid for it
> 3) add the nhx species tag
> 4) write the nhx tree
> 
> I was able to do the first 2 steps, and I could create an object 
> node_nhx and add the tag T,
> but I don't know how to write an nhx Tree with the node_nhx previously 
> created...
> 
> Does anyone have an idea? any help are welcome.
> 
> Thanks,
> 
> laurence.
> 
> 
> Here are my code and the samples files for better understanding:
> newick2nhx.pl -f test_tree.nwk -o tata -c seq_taxid.txt
> 
> _newick2nhx.pl:_
> use strict;
> use Bio::TreeIO;
> use Bio::Tree::NodeNHX;
> use Getopt::Long;
> 
> 
> my $tree_file;
> my $outfile;
> my $codefile;
> my %corresp;
> 
> GetOptions('f|file:s' =>\$tree_file, 'o|out:s' =>\$outfile, 'c|code:s' 
> =>\$codefile);
> 
> open (CODE, "< $codefile");
> while (<CODE>)
> {
>     chomp;
>     my($a, $b)=split (/\t/);
>     $corresp{$a}=$b;
> }
> 
> 
> my $treeio = new Bio::TreeIO (-format => 'newick', -file => 
"$tree_file");
> my $treeout= new Bio::TreeIO (-format => 'nhx', -file =>">$outfile");
> 
> while (my $tree= $treeio->next_tree)
> {
>     my @nodes=$tree->get_nodes();
>     foreach my $nd(@nodes)
>     {
>         if ($nd->is_Leaf())
>         {
>             my $id=$nd->id();
>             print "$id TAXID ",$corresp{$id},"\n";
> 
>             my $nodenhx=new Bio::Tree::NodeNHX();
>             $nodenhx->nhx_tag({T=>$corresp{$id}});
>         }
>     }
>     $treeout->write_tree($tree);
> }
> 
> 
> _test_tree.nwk_:
> 
(((((42558930:100.0,42558943:100.0):100.0,(42558969:100.0,(42558981:100.0,
> 
42558942:100.0):100.0):72.0):81.0,(((((90185247:100.0,56405380:100.0):100.0,
> (42558987:100.0,148887393:100.0):100.0):90.0,66774197:100.0):100.0,
> AAEL015662:100.0):100.0,
> 42558970:100.0):82.0):100.0,(42558929:100.0,42558958:100.0):79.0):100.0,
> 42558941:100.0);
> 
> _seq_taxid.txt:_
> AAEL015662      7159
> 42558969        9606
> 42558981        10090
> 42558942        9606
> 42558970        6239
> 42558929        10116
> 42558987        9606
> 42558930        10116
> 42558943        9606
> 148887393       10090
> 42558958        10090
> 42558941        9606
> 56405380        10090
> 90185247        9606
> 66774197        6239
> 
> 
> _And the tata resulting file:_
> (((((42558930:100.0,42558943:100.0):100.0[&&NHX],(42558969:100.0,
> 
(42558981:100.0,42558942:100.0):100.0[&&NHX]):72.0[&&NHX]):81.0[&&NHX],(((((
> 90185247:100.0,56405380:100.0):100.0[&&NHX],(42558987:100.0,
> 148887393:100.0):100.0[&&NHX]):90.0[&&NHX],66774197:100.0):100.
> 0[&&NHX],AAEL01566
> 2:100.0):100.0[&&NHX],42558970:100.0):82.0[&&NHX]):100.0[&&NHX],
> 
(42558929:100.0,42558958:100.0):79.0[&&NHX]):100.0[&&NHX],42558941:100.0);
> 
> 
> 
> 
> -- 
> ====================================================================
> = Laurence Amilhat    INRA Toulouse 31326 Castanet-Tolosan           = 
> = Tel: 33 5 61 28 53 34   Email: laurence.amilhat at toulouse.inra.fr =
> ====================================================================
> 
> 
> 
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