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Chaos.pm

Bio::Chaos - utility class for handling Chaos-XML =head1 SYNOPSIS


NAME


  Bio::Chaos              - utility class for handling Chaos-XML

   

=head1 SYNOPSIS

  use Bio::Chaos;

  my $C = Bio::Chaos->new;

  $C->parse('test.gff');

  $C->set_organism('Drosophila melanogaster');

  print $C->transform_to('chadoxml')->xml;

  

=cut


DESCRIPTION

This module contains some basic methods for manipulating a Chaos-XML document stored in memory as a the Data::Stag manpage tree. This class is fairly minimal. One of the principal ideas being the Bio::Chaos manpage is that access to the data model should be directly through generic XML-based data accessors, such as those provided by the Data::Stag manpage

For more advanced functionality, see the Bio::Chaos::ChaosGraph manpage - this augments the generic accessor methods with some sequence feature semantics, and methods for graph traversal, location transformation etc

root


 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

parse


 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 the Bio::Chaos::Parser manpage for details of the parsing architecture

transform_to


  Usage   - $C->transform_to('chadoxml');

  Returns -

  Args    - fmt str

applies a transformation to the chaos node in memory

set_organism


  Usage   - $C->set_organism('Drosophila melanogaster')

  Returns -

  Args    - org str

Sets organism_id for ALL features in the document

new_feature


 Usage   - my $f = Data::Stag->new_feature

 Returns - L<Data::Stag> feature node

 Args    -
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