Bio::Chaos - utility class for handling Chaos-XML
use Bio::Chaos; my $C = Bio::Chaos->new; $C->parse('test.gff'); $C->set_organism('Drosophila melanogaster'); print $C->transform_to('chadoxml')->xml;
This module contains some basic methods for manipulating a Chaos-XML document stored in memory as a Data::Stag tree. This class is fairly minimal. One of the principal ideas being Bio::Chaos is that access to the data model should be directly through generic XML-based data accessors, such as those provided by Data::Stag
For more advanced functionality, see Bio::Chaos::ChaosGraph - this augments the generic accessor methods with some sequence feature semantics, and methods for graph traversal, location transformation etc
Usage - my $cx = $C->root; Returns - L<Data::Stag> chaos node Args -
returns the top-level of the Chaos-XML document as a stag tree
Usage - my $cx = $C->parse('sample_data/Rab1.chaos'); Usage - my $cx = $C->parse('t/data/AE003744.gbk','genbank'); Usage - my $cx = $C->parse('t/data/test.chado','chado'); Usage - my $cx = $C->parse('t/data/foo.gff','gff3'); Returns - L<Data::Stag> chaos node Args - file str format str
parses from various formats into an in-memory chaos-xml file
see Bio::Chaos::Parser for details of the parsing architecture
Usage - $C->transform_to('chadoxml'); Returns - Args - fmt str
applies a transformation to the chaos node in memory
Usage - $C->set_organism('Drosophila melanogaster') Returns - Args - org str
Sets organism_id for ALL features in the document
Usage - my $f = Data::Stag->new_feature Returns - L<Data::Stag> feature node Args -
To install Bio::Chaos, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Chaos
CPAN shell
perl -MCPAN -e shell install Bio::Chaos
For more information on module installation, please visit the detailed CPAN module installation guide.