NAME

Bio::Phylo::Parsers::Json - Parser used by Bio::Phylo::IO, no serviceable parts inside

DESCRIPTION

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.

SEE ALSO

Bio::Phylo::IO

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

Bio::Phylo::Manual

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

CITATION

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