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Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset

Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset


NAME


  Bio::Chaos::ChaosGraph     - object for representing a chaos-xml dataset


SYNOPSIS


  use Bio::Chaos::ChaosGraph;

  use Data::Stag;

  my $chaos_node = Data::Stag->parse('Rab1.chaos');

  my $cg = Bio::Chaos::ChaosGraph->new($chaos_node);

  

  my $fl = $cg->top_features;

  foreach my $f (@$fl) {

    next unless $f->get_type eq 'gene';

    $island_feature = $cg->make_gene_island($f, 5000, 5000);

    print $island_feature->xml;

  }


DESCRIPTION

This class allows manipulation of in-memory Chaos documents as the Data::Stag manpage nodes, and provides additional methods for traversing the graph structure defined in the Chaos document


SEE ALSO

The cx-genbank2chaos.pl script

The the Bio::Chaos manpage helper module

The BioPerl the Bio::SeqIO::chaosxml manpage writer

new


  Usage   - my $chaos = Bio::Chaos::ChaosGraph->new($chaos_stag)

  Returns - Bio::Chaos::ChaosGraph

creates a new Chaos::ChaosGraph object

init_from_stag


  Usage   - $cg->init_from_stag($chaos_node);

  Returns -

  Args    - L<Data::Stag>

sets up a CG object from a stag node conforming to the Chaos-XML schema


  my $cg = Bio::Chaos::ChaosGraph->new;

  my $cn = Data::Stag->parse("mydata.chaos.xml");

  $cg->init_from_stag($cn);

init_from_file


  Usage   - $cg->init_from_file($chaos_node);

  Returns -

  Args    - filename string

sets up a CG object from a file conforming to the Chaos-XML schema


  my $cg = Bio::Chaos::ChaosGraph->new;

  $cg->init_from_file("mydata.chaos.xml");

stag


 Usage   - my $chaos_node = $cg->stag;

 Returns - L<Data::Stag>

 Args    -

Generates a the Data::Stag manpage object conforming to Chaos-XML dtd

unflattener


  Usage   - my $unf = $cg->unflattener;

  Usage   - $cg->unflattener(Bio::SeqFeature::Tools::Unflattener->new);

  Returns - L<Bio::SeqFeature::Tools::Unflattener>

  Args    - L<Bio::SeqFeature::Tools::Unflattener> (OPTIONAL)

gets/sets the object that the CG will use for unflattening genbank seqs. See bioperl docs for details

type_mapper


  Usage   - my $unf = $cg->type_mapper;

  Usage   - $cg->type_mapper(Bio::SeqFeature::Tools::Type_mapper->new);

  Returns - L<Bio::SeqFeature::Tools::Type_mapper>

  Args    - L<Bio::SeqFeature::Tools::Type_mapper> (OPTIONAL)

gets/sets the object that the CG will use for mapping genbank types to SO. See bioperl docs for details

feature_idx


 Usage   - my $f = $cg->feature_idx->{$feature_id}

 Returns - hashref, keyed by feature ID

 Args    -

index hash for looking up feature stag nodes by ID

The ID is the value of feature/feature_id in the chaos-xml structure

the hash has values that are chaos the Data::Stag manpage nodes, and can be accessed using normal stag methods/functions

get_feature


 Usage   - my $f = $cg->get_feature($feature_id)

 Returns - L<Data::Stag> conforming to Chaos-xml feature element

 Args    - id string

look up feature stag nodes by ID

The ID is the value of feature/feature_id in the chaos-xml structure

The returned the Data::Stag manpage node is a feature node/element, and can be accessed using normal stag methods/functions

graph


  Usage   - my $graph = $cg->graph;

  Returns - L<Graph>

  Args    -

gets/sets the Graph object which corresponds to the graph defined by the chado/chaos feature_relationships. The sink of the graph is the root (eg genes), the source of the graph is the leaves (eg exons).

The graph labels contain the relationship type and the rank

You should not need to manipulate the Graph object directly - this is mostly used internally, but is made public to allow inspection of the graph using the native Graph methods

graph


  Usage   - my $locgraph = $cg->locgraph;

  Returns - L<Graph>

  Args    -

gets/sets the Graph object which corresponds to the graph defined by the chado/chaos featurelocs.

The graph labels contain the nbeg, nend, rank, group

You should not need to manipulate the Graph object directly - this is mostly used internally, but is made public to allow inspection of the graph using the native Graph methods

add_feature


 Usage   - $cg->add_feature($f);

 Returns -

 Args    - L<Data::Stag> [feature node]

add_featureloc


 Usage   - $cg->add_featureloc($fl);

 Returns -

 Args    - L<Data::Stag> [featureloc node]

replace_featureloc


  Usage   - $cg->replace_featureloc($f,$fl_old,$fl_new);

  Returns -

  Args    - feature L<Data::Stag> [feature node]

            old loc L<Data::Stag> [featureloc node]

            new loc L<Data::Stag> [featureloc node]

add_feature_relationship


 Usage   - $cg->add_feature_relationship($f);

 Returns -

 Args    - L<Data::Stag> [feature_relationship node]

top_features


  Usage   - my $features = $cg->top_features;

  Returns - listref of L<Data::Stag> feature nodes

  Args    -

returns features at the root of the feature graph (typically genes, but also ``simple'' features that are not attached other features via feature_relationships, such as SNPs, contigs, etc

Formally, a feature F is a top feature if there is no feature_relationship R with R.subject_id = F

leaf_features


  Usage   - my $features = $cg->leaf_features;

  Returns - listref of L<Data::Stag> feature nodes

  Args    -

returns features at the leaves of the feature graph (with gene model subgraphs, these may be exons and polypeptides - or ``simple'' features that are not attached other features via feature_relationships, such as SNPs, contigs, etc)

Formally, a feature F is a leaf feature if there is no feature_relationship R with R.object_id = F

unlocalised_features


  Usage   - my $topfs = $cg->unlocalised_features;

  Synonym - unlocalized_features

  Returns - listref of L<Data::Stag> feature nodes

  Args    -

returns features at the root of the featureloc graph, ie unlocalised features.

Formally, a feature F is unlocalised if it contains no featurelocs

top_unlocalised_features


  Usage   - my $topfs = $cg->top_unlocalised_features;

  Synonym - top_unlocalized_features

  Returns - listref of L<Data::Stag> feature nodes

  Args    -

Returns the intersection of the set of all unlocalised features and all top features

get_features_on


  Usage   - my $features = $cg->get_features_on($contig_feature)

  Returns - listref of L<Data::Stag> feature nodes

  Args    - L<Data::Stag> feature node OR id string

all features DIRECTLY localised to a particular feature

get_features_contained_by


  Usage   - my $transcripts = $cg->get_features_contained_by($gene_feature)

  Returns - listref of L<Data::Stag> feature nodes

  Args    - L<Data::Stag> feature node

all features contained by another feature, where containment is defined by any feature_relationship, with the container being the object_id and the containee being the subject_id. feature_relationship.type is ignored

get_features_containing


  Usage   - my $transcripts = $cg->get_features_containing($exon_feature)

  Returns - listref of L<Data::Stag> feature nodes

  Args    - L<Data::Stag> feature node

all features containing by another feature, where containment is defined by any feature_relationship, with the container being the object_id and the containee being the subject_id. feature_relationship.type is ignored

get_all_contained_features


  Usage   - my $features = $cg->get_all_contained_features($gene_feature)

  Returns - listref of L<Data::Stag> feature nodes

  Args    - L<Data::Stag> feature node

As get_features_contained_by, but performs the transitive closure - eg for a gene will fetch transcriipts, and the transcripts subfeatures (exons) into one flat list

feature_relationships_for_subject


 Usage   - $frs = $cg->get_feature_relationships_for_subject($exon_id);

 Returns - listref of L<Data::Stag> feature_relationship nodes

 Args    - L<Data::Stag> feature node OR id string

find the feature_relationship nodes with a particular subject_id

make_gene_islands


 Usage   - my $contigs = $cg->make_gene_islands;

 Returns - listref of L<Data::Stag> feature nodes

 Args    -

create a contig feature for every gene, and transform the gene and all the subfeatures of gene onto that contig

derive_residues


 Usage   - my $ok = $cg->derive_residues($feature);

 Returns - sequence string

 Returns - L<Data::Stag> feature node

splices out the residues from the srcfeature and sets the feature/residues element (does not return the actual residues)

loctransform


 Usage   - $cg->loctransform($gene,$contig);

 Args    - source L<Data::Stag> feature node

           target L<Data::Stag> feature node

replaces the featureloc(s) of a feature with new featureloc(s) relative to the target feature - eg going from chromosome to contig

get_features_by_type


 Usage   - my $exons = $cg->get_features_by_type('exon');

 Returns - listref of L<Data::Stag> feature nodes

 Args    - type string

gets features by type (exact - does not traverse ontology graph)

get_features


 Usage   - my $features = $cg->get_features;

 Returns - listref of L<Data::Stag> feature nodes

 Args    - none

returns all features

name_all_features


 Usage   - $cg->name_all_features

 Returns -

 Args    -

makes sure all feature have names. will not affect features that already have names

sets both feature/name and feature/uniquename

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