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Author image Rutger Vos
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Bio::Phylo::Parsers::Json - Parser used by Bio::Phylo::IO, no serviceable parts inside


This module is used to import NeXML data that was re-formatted as JSON, using the mapping implemented by XML::XML2JSON. This module is experimental in that complex NeXML-to-JSON mapped strings may fail to yield valid NeXML (and, consequently, valid Bio::Phylo objects) in the round trip. The reason for this is that the XML2JSON omits xmlns declarations in its JSON output. We try to work around this here by re-introducing the default namespaces, but if any additional ones were present in the original NeXML (e.g. to specify namspaces for metadata predicates) these can't be reconstructed. In addition, the JSON that XML2JSON produces doesn't preserve element order. We try to be lenient about this when parsing the intermediate NeXML, though it is actually invalid.


There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.


The json parser is called by the Bio::Phylo::IO object. Look there to learn how to parse data using Bio::Phylo.


Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com


If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63