Error with TreeIO for NHX format

[cjfields]

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Author Name: Ameet Talwalkar (Ameet Talwalkar) Original Redmine Issue: 3149, https://redmine.open-bio.org/issues/3149 Original Date: 2010-10-27 Original Assignee: Chris Fields

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I would like to use BIOPerl to convert a tree in PhyloXML format to NHX format, and I have tried the following code:

use Bio::TreeIO;

my $input = new Bio::TreeIO(-file => “reconciled_test.xml”, -format => “phyloxml”); my $treeout = new Bio::TreeIO(-fh => *STDOUT, -format => ‘nhx’);

while (my $tree = $input->next_tree) { $treeout->write_tree($tree); }

The output is indeed in NHX format, but the tags (in particular I have a duplication / speciation tag) do not appear in the output. I sent an email to bioperl-l@bioperl.org to ask for help, and was contacted by Chris Fields, who suggested that I file a bug report, as he suggested that “it’s possible the tags are parsed but the NHX writer is not finding the data somehow.”

[cjfields]

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Original Redmine Comment Author Name: Ameet Talwalkar Original Date: 2010-10-27T00:11:24Z

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Created an attachment (id=1547) perl script using bioperl that incorrectly converts phyloxml to nhx

[cjfields]

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Original Redmine Comment Author Name: Ameet Talwalkar Original Date: 2010-10-27T00:12:44Z

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Created an attachment (id=1548) intial phyloxml tree

[cjfields]

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Original Redmine Comment Author Name: Ameet Talwalkar Original Date: 2010-10-27T00:15:59Z

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Created an attachment (id=1549) Desired tree in NHX format created via Archaeopteryx (GUI for Forester)

[cjfields]

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Original Redmine Comment Author Name: Ameet Talwalkar Original Date: 2010-10-27T00:17:14Z

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Created an attachment (id=1550) Output of perl script, containing nhx tree WITHOUT relevant tags.

[cjfields]

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Original Redmine Comment Author Name: Chris Fields Original Date: 2011-03-05T22:24:06Z

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Strangely, this was reported as a FeatureIO bug. Moving back.

[cjfields]

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Original Redmine Comment Author Name: Chris Fields Original Date: 2011-03-11T20:45:25Z

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wubba (test commit for guts)