[Bioperl-l] parsing a phyloxml file

Chrysanthi A. chrysain at gmail.com
Wed Jan 28 10:40:17 EST 2009


Hi,

I am trying to parse a phyloxml file but I get the message error below:

Bio::TreeIO: phyloxml cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use
XML::LibXML::Reader module - your libxml2 is compiled without reader
support! at
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm
line 17
BEGIN failed--compilation aborted at
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm
line 17.
Compilation failed in require at
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline
73.
BEGIN failed--compilation aborted at
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline
73.
Compilation failed in require at
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm line
420.

STACK Bio::Root::Root::_load_module
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm:422
STACK (eval)
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:230
STACK Bio::TreeIO::_load_format_module
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:229
STACK Bio::TreeIO::new
/System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:124
STACK toplevel parse.pl:1
-------------------------------------


For more information about the TreeIO system please see the TreeIO docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_tree" on an undefined value at parse.pl line 1.


Does anyone can help me?

Thanks a lot,

Chrysanht


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