Bio::SeqFeature::Computation.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqFeature::Computation - Computation SeqFeature

SYNOPSIS

    $feat = Bio::SeqFeature::Computation->new(
                                 -start => 10, -end => 100,
                                 -strand => -1, -primary => 'repeat',
                                 -program_name => 'GeneMark',
                                 -program_date => '12-5-2000',
                                 -program_version => 'x.y',
                                 -database_name => 'Arabidopsis',
                                 -database_date => '12-dec-2000',
                                 -computation_id => 2231,
                                 -score    => { no_score => 334 } );
 
 

DESCRIPTION

Bio::SeqFeature::Computation extends the Generic seqfeature object with a set of computation related fields and a more flexible set of storing more types of score and subseqfeatures. It is compatible with the Generic SeqFeature object.

The new way of storing score values is similar to the tag structure in the Generic object. For storing sets of subseqfeatures the array containg the subseqfeatures is now a hash which contains arrays of seqfeatures Both the score and subSeqfeature methods can be called in exactly the same way, the value's will be stored as a 'default' score or subseqfeature.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Ewan Birney, Mark Fiers

Ewan Birney <birney@sanger.ac.uk> Mark Fiers <m.w.e.j.fiers@plant.wag-ur.nl>

DEVELOPERS

This class has been written with an eye out of inheritance. The fields the actual object hash are:
    _gsf_sub_hash  = reference to a hash containing sets of sub arrays
    _gsf_score_hash= reference to a hash for the score values
 
 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

has_score

  Title   : has_score
  Usage   : $value = $self->has_score('some_score')
  Function: Tests wether a feature contains a score
  Returns : TRUE if the SeqFeature has the score,
            and FALSE otherwise.
  Args    : The name of a score
 
 

add_score_value

  Title   : add_score_value
  Usage   : $self->add_score_value('P_value',224);
  Returns : TRUE on success
  Args    : score (string) and value (any scalar)
 
 

score

  Title   : score
  Usage   : $value = $comp_obj->score()
            $comp_obj->score($value)
  Function: Returns the 'default' score or sets the 'default' score
            This method exist for compatibility options           
            It would equal ($comp_obj->each_score_value('default'))[0];
  Returns : A value
  Args    : (optional) a new value for the 'default' score
 
 

each_score_value

  Title   : each_score_value
  Usage   : @values = $gsf->each_score_value('note');
  Function: Returns a list of all the values stored
            under a particular score.
  Returns : A list of scalars
  Args    : The name of the score
 
 

all_scores

  Title   : all_scores
  Usage   : @scores = $feat->all_scores()
  Function: Get a list of all the scores in a feature
  Returns : An array of score names
  Args    : none
 
 

remove_score

  Title   : remove_score
  Usage   : $feat->remove_score('some_score')
  Function: removes a score from this feature
  Returns : nothing
  Args    : score (string)
 
 

computation_id

  Title   : computation_id
  Usage   : $computation_id = $feat->computation_id()
            $feat->computation_id($computation_id)
  Function: get/set on program name information
  Returns : string
  Args    : none if get, the new value if set
 
 

program_name

  Title   : program_name
  Usage   : $program_name = $feat->program_name()
            $feat->program_name($program_name)
  Function: get/set on program name information
  Returns : string
  Args    : none if get, the new value if set
 
 

program_date

  Title   : program_date
  Usage   : $program_date = $feat->program_date()
            $feat->program_date($program_date)
  Function: get/set on program date information
  Returns : date (string)
  Args    : none if get, the new value if set
 
 

program_version

  Title   : program_version
  Usage   : $program_version = $feat->program_version()
            $feat->program_version($program_version)
  Function: get/set on program version information
  Returns : date (string)
  Args    : none if get, the new value if set
 
 

database_name

  Title   : database_name
  Usage   : $database_name = $feat->database_name()
            $feat->database_name($database_name)
  Function: get/set on program name information
  Returns : string
  Args    : none if get, the new value if set
 
 

database_date

  Title   : database_date
  Usage   : $database_date = $feat->database_date()
            $feat->database_date($database_date)
  Function: get/set on program date information
  Returns : date (string)
  Args    : none if get, the new value if set
 
 

database_version

  Title   : database_version
  Usage   : $database_version = $feat->database_version()
            $feat->database_version($database_version)
  Function: get/set on program version information
  Returns : date (string)
  Args    : none if get, the new value if set
 
 

sub_SeqFeature_type

  Title   : sub_SeqFeature_type
  Usage   : $sub_SeqFeature_type = $feat->sub_SeqFeature_type()
            $feat->sub_SeqFeature_type($sub_SeqFeature_type)
  Function: sub_SeqFeature_type is automatically set when adding
            a sub_computation (sub_SeqFeature) to a computation object
  Returns : sub_SeqFeature_type (string)
  Args    : none if get, the new value if set
 
 

all_sub_SeqFeature_types

  Title   : all_Sub_SeqFeature_types
  Usage   : @all_sub_seqfeature_types = $comp->all_Sub_SeqFeature_types();
  Function: Returns an array with all subseqfeature types
  Returns : An array
  Args    : none
 
 

sub_SeqFeature

  Title   : sub_SeqFeature('sub_feature_type')
  Usage   : @feats = $feat->sub_SeqFeature();
            @feats = $feat->sub_SeqFeature('sub_feature_type');           
  Function: Returns an array of sub Sequence Features of a specific
            type or, if the type is ommited, all sub Sequence Features
  Returns : An array
  Args    : (optional) a sub_SeqFeature type (ie exon, pattern)
 
 

add_sub_SeqFeature

  Title   : add_sub_SeqFeature
  Usage   : $feat->add_sub_SeqFeature($subfeat);
            $feat->add_sub_SeqFeature($subfeat,'sub_seqfeature_type')
            $feat->add_sub_SeqFeature($subfeat,'EXPAND')
            $feat->add_sub_SeqFeature($subfeat,'EXPAND','sub_seqfeature_type')
  Function: adds a SeqFeature into a specific subSeqFeature array.
            with no 'EXPAND' qualifer, subfeat will be tested
            as to whether it lies inside the parent, and throw
            an exception if not.
            If EXPAND is used, the parents start/end/strand will
            be adjusted so that it grows to accommodate the new
            subFeature,
            optionally a sub_seqfeature type can be defined.
  Returns : nothing
  Args    : An object which has the SeqFeatureI interface
          : (optional) 'EXPAND'
          : (optional) 'sub_SeqFeature_type'
 
 

flush_sub_SeqFeature

  Title   : flush_sub_SeqFeature
  Usage   : $sf->flush_sub_SeqFeature
            $sf->flush_sub_SeqFeature('sub_SeqFeature_type');    
  Function: Removes all sub SeqFeature or all sub SeqFeatures
            of a specified type 
            (if you want to remove a more specific subset, take
             an array of them all, flush them, and add
             back only the guys you want)
  Example :
  Returns : none
  Args    : none