[Bioperl-l] SVG treefile problem
Amanda O'Reilly
ajo11 at mole.bio.cam.ac.uk
Thu Jan 19 12:02:47 UTC 2006
I am trying to draw SVG format phylogenetic trees - the output tree is
distorted.
Using checked code & tree from here (code reproduced below also):
http://portal.open-bio.org/pipermail/bioperl-l/2004-April/015581.html
This gives a distorted tree if I leave out 'warn $tree'.
If I leave 'warn $tree' in the code, I get the following error.
Bio::Tree::Tree=HASH(0x606b68) at tree_play.pl line 17, <GEN0> line 1.
Have tried running with UNIX (BioPerl 1.5) & Linux installations & tried
viewing tree with different applications- output tree always looks wrong.
Thanks,
Amanda.
#!/usr/local/bin/perl -w
use strict;
use lib '.';
use Bio::TreeIO;
use Data::Dumper;
use SVG::Graph;
my $infile = "/scratch/ajo11/exp/aln/000ms/11.ph";
my $outfile = ">/scratch/ajo11/exp/aln/000ms/11.svg";
my $in = new Bio::TreeIO(-file => $infile,
-format => 'newick');
my $out = new Bio::TreeIO(-file => $outfile,
-format => 'svggraph');
while( my $tree = $in->next_tree ) {
#warn $tree;
my $svg_xml = $out->write_tree($tree);
}
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