NAME

Bio::Chado::Schema::Result::Sequence::Feature

DESCRIPTION

A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.

ACCESSORS

feature_id

data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'feature_feature_id_seq'

dbxref_id

data_type: 'integer'
is_foreign_key: 1
is_nullable: 1

An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.

organism_id

data_type: 'integer'
is_foreign_key: 1
is_nullable: 0

The organism to which this feature belongs. This column is mandatory.

name

data_type: 'varchar'
is_nullable: 1
size: 255

The optional human-readable common name for a feature, for display purposes.

uniquename

data_type: 'text'
is_nullable: 0

The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.

residues

data_type: 'text'
is_nullable: 1

A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.

seqlen

data_type: 'integer'
is_nullable: 1

The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.

md5checksum

data_type: 'char'
is_nullable: 1
size: 32

The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.

type_id

data_type: 'integer'
is_foreign_key: 1
is_nullable: 0

A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.

is_analysis

data_type: 'boolean'
default_value: false
is_nullable: 0

Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.

is_obsolete

data_type: 'boolean'
default_value: false
is_nullable: 0

Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.

timeaccessioned

data_type: 'timestamp'
default_value: current_timestamp
is_nullable: 0
original: {default_value => \"now()"}

For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.

timelastmodified

data_type: 'timestamp'
default_value: current_timestamp
is_nullable: 0
original: {default_value => \"now()"}

RELATIONS

analysisfeatures

Type: has_many

cell_line_features

Type: has_many

elements

Type: has_many

type

Type: belongs_to

dbxref

Type: belongs_to

organism

Type: belongs_to

feature_cvterms

Type: has_many

feature_dbxrefs

Type: has_many

feature_expressions

Type: has_many

feature_genotype_features

Type: has_many

feature_genotype_chromosomes

Type: has_many

featureloc_features

Type: has_many

featureloc_srcfeatures

Type: has_many

feature_phenotypes

Type: has_many

featurepos_feature

Type: has_many

featurepos_map_features

Type: has_many

featureprops

Type: has_many

feature_pubs

Type: has_many

featurerange_leftendfs

Type: has_many

featurerange_rightstartfs

Type: has_many

featurerange_rightendfs

Type: has_many

featurerange_leftstartfs

Type: has_many

featurerange_features

Type: has_many

feature_relationship_subjects

Type: has_many

feature_relationship_objects

Type: has_many

feature_synonyms

Type: has_many

library_features

Type: has_many

phylonodes

Type: has_many

studyprop_features

Type: has_many

ADDITIONAL RELATIONSHIPS

parent_relationships

Type: has_to_many

Returns a list of parent relationships.

Related object: Bio::Chado::Schema::Result::Sequence::FeatureRelationship

child_relationships

Type: has_to_many

Returns a list of child relationships.

Related object: Bio::Chado::Schema::Result::Sequence::FeatureRelationship

primary_dbxref

Alias for dbxref

MANY-TO-MANY RELATIONSHIPS

parent_features

Type: many_to_many

Returns a list of parent features (i.e. features that are the object of feature_relationship rows in which this feature is the subject).

Related object: Bio::Chado::Schema::Result::Sequence::Feature

child_features

Type: many_to_many

Returns a list of child features (i.e. features that are the subject of feature_relationship rows in which this feature is the object).

Related object: Bio::Chado::Schema::Result::Sequence::Feature

synonyms

Type: many_to_many

dbxrefs_mm

Type: many_to_many

Related object: Bio::Chado::Schema::Result::General::Dbxref (i.e. dbxref table) Bio::Chado::Schema::Result::Sequence::FeatureDbxref (feature_dbxref table)

secondary_dbxrefs

Alias for dbxrefs_mm

ADDITIONAL METHODS

create_featureprops

Usage: $set->create_featureprops({ baz => 2, foo => 'bar' });
Desc : convenience method to create feature properties using cvterms
        from the ontology with the given name
Args : hashref of { propname => value, ...},
       options hashref as:
        {
          autocreate => 0,
             (optional) boolean, if passed, automatically create cv,
             cvterm, and dbxref rows if one cannot be found for the
             given featureprop name.  Default false.

          cv_name => cv.name to use for the given featureprops.
                     Defaults to 'feature_property',

          db_name => db.name to use for autocreated dbxrefs,
                     default 'null',

          dbxref_accession_prefix => optional, default
                                     'autocreated:',
          definitions => optional hashref of:
              { cvterm_name => definition,
              }
           to load into the cvterm table when autocreating cvterms

           allow_duplicate_values => default false.
              If true, allow duplicate instances of the same cvterm
              and value in the properties of the feature.  Duplicate
              values will have different ranks.
        }
Ret  : hashref of { propname => new featureprop object }

search_featureprops

Status  : public
Usage   : $feat->search_featureprops( 'description' )
          # OR
          $feat->search_featureprops({ name => 'description'})
Returns : DBIx::Class::ResultSet like other search() methods
Args    : single string to match cvterm name,
          or hashref of search criteria.  This is passed
          to $chado->resultset('Cv::Cvterm')
                   ->search({ your criteria })

Convenience method to search featureprops for a feature that
match to Cvterms having the given criterion hash

Bio::PrimarySeqI METHODS

The methods below are intended to provide some compatibility with BioPerl's Bio::PrimarySeqI interface, so that a feature may be used as a sequence. Note that Bio::PrimarySeqI only provides identifier, accession, and sequence information, no subfeatures, ranges, or the like.

Support for BioPerl's more complete Bio::SeqI interface, which includes those things, still needs to be implemented. If you are interested in helping with this, please contact GMOD!

id, primary_id, display_id

These are aliases for name(), which just returns the contents of the feature.name field

seq

Alias for $feature->residues()

subseq( $start, $end )

Same as Bio::PrimarySeq subseq method, with one important exception. If the residues column is not set (null) for this feature, it checks for a featureprop of type large_residues (irrespective of the type's CV membership), and uses its value as the sequence if it is present.

So, you can store large (i.e. megabase or greater) sequences in a large_residues featureprop, and use this subseq() method to fetch pieces of them, with the sequences never being entirely stored in memory or transferred in total from the database server to the app server. This is implemented behind the scenes by using SQL substring operations on the featureprop's value.

trunc

Same as subseq above, but return a sequence object rather than a bare string.

accession, accession_number

Usage: say $feature->accession_number
Desc : get an "<accession>.<version>"-style string.  gets this from
       either the primary dbxref, or the first secondary_dbxref
       found
Args : none
Ret : string of the form "accession.version" formed from the
      accession and version fields of either the primary or
      secondary dbxrefs

length

No arguments, returns the seqlen(), or length( $feature->residues ) if that is not defined.

desc, description

No arguments, returns the value of the first 'description' featureprop found for this feature.

alphabet

Returns "protein" if the feature's type name is "polypeptide". Otherwise, returns "dna". This is not very correct, but works in most of the use cases we've seen so far.

To install Bio::Chado::Schema, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Chado::Schema

CPAN shell

perl -MCPAN -e shell
install Bio::Chado::Schema

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

DESCRIPTION

ACCESSORS

feature_id

dbxref_id

organism_id

name

uniquename

residues

seqlen

md5checksum

type_id

is_analysis

is_obsolete

timeaccessioned

timelastmodified

RELATIONS

analysisfeatures

cell_line_features

elements

type

dbxref

organism

feature_cvterms

feature_dbxrefs

feature_expressions

feature_genotype_features

feature_genotype_chromosomes

featureloc_features

featureloc_srcfeatures

feature_phenotypes

featurepos_feature

featurepos_map_features

featureprops

feature_pubs

featurerange_leftendfs

featurerange_rightstartfs

featurerange_rightendfs

featurerange_leftstartfs

featurerange_features

feature_relationship_subjects

feature_relationship_objects

feature_synonyms

library_features

phylonodes

studyprop_features

ADDITIONAL RELATIONSHIPS

parent_relationships

child_relationships

primary_dbxref

MANY-TO-MANY RELATIONSHIPS

parent_features

child_features

synonyms

dbxrefs_mm

secondary_dbxrefs

ADDITIONAL METHODS

create_featureprops

search_featureprops

Bio::PrimarySeqI METHODS

id, primary_id, display_id

seq

subseq( $start, $end )

trunc

accession, accession_number

length

desc, description

alphabet

Module Install Instructions