Bio::Seq::RichSeq.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry

SYNOPSIS

See Bio::Seq::RichSeqI and documentation of methods.

DESCRIPTION

This module implements Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided.

Implemented Interfaces

This class implementes the following interfaces.
Bio::Seq::RichSeqI
Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI.
Bio::IdentifiableI
Bio::DescribableI
Bio::AnnotatableI

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

Email birney@ebi.ac.uk

APPENDIX

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

new

  Title   : new
  Usage   : $seq    = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
                                              -id  => 'human_id',
                                              -accession_number => 'AL000012',
                                             );
 
  Function: Returns a new seq object from
            basic constructors, being a string for the sequence
            and strings for id and accession_number
  Returns : a new Bio::Seq::RichSeq object
 
 

division

  Title   : division
  Usage   : $obj->division($newval)
  Function: 
  Returns : value of division
  Args    : newvalue (optional)
 
 

molecule

  Title   : molecule
  Usage   : $obj->molecule($newval)
  Function: 
  Returns : type of molecule (DNA, mRNA)
  Args    : newvalue (optional)
 
 

add_date

  Title   : add_date
  Usage   : $self->add_date($datestr)
  Function: adds one or more dates
 
            This implementation stores dates as keyed annotation, the
            key being 'date_changed'. You can take advantage of this
            fact when accessing the annotation collection directly.
 
  Example :
  Returns : 
  Args    : a date string or an array of such strings
 
 

get_dates

  Title   : get_dates
  Usage   : my @dates = $seq->get_dates;
  Function: Get the dates of the sequence (usually, when it was created and
            changed.
  Returns : an array of date strings
  Args    :
 
 

pid

  Title   : pid
  Usage   : my $pid = $seq->pid();
  Function: Get (and set, depending on the implementation) the PID property
            for the sequence.
  Returns : a string
  Args    :
 
 

accession

  Title   : accession
  Usage   : $obj->accession($newval)
  Function: Whilst the underlying sequence object does not 
            have an accession, so we need one here.
 
            In this implementation this is merely a synonym for
            accession_number().
  Example : 
  Returns : value of accession
  Args    : newvalue (optional)
 
 

add_secondary_accession

  Title   : add_secondary_accession
  Usage   : $self->add_domment($ref)
  Function: adds a secondary_accession
 
            This implementation stores secondary accession numbers as
            keyed annotation, the key being 'secondary_accession'. You
            can take advantage of this fact when accessing the
            annotation collection directly.
 
  Example :
  Returns : 
  Args    : a string or an array of strings
 
 

get_secondary_accessions

  Title   : get_secondary_accessions
  Usage   : my @acc = $seq->get_secondary_accessions();
  Function: Get the secondary accession numbers as strings.
  Returns : An array of strings
  Args    : none
 
 

seq_version

  Title   : seq_version
  Usage   : $obj->seq_version($newval)
  Function: Get/set the sequence version
  Returns : value of seq_version (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

add_keyword

  Title   : add_keyword
  Usage   : $obj->add_keyword($newval)
  Function: Add a new keyword to the annotation of the sequence.
 
            This implementation stores keywords as keyed annotation,
            the key being 'keyword'. You can take advantage of this
            fact when accessing the annotation collection directly.
 
  Returns : 
  Args    : value to be added (optional) (a string)
 
 

get_keywords

  Title   : get_keywords
  Usage   : $obj->get_keywords($newval)
  Function: Get the keywords for this sequence as an array of strings.
  Returns : an array of strings
  Args    :
 
 

Private methods and synonyms for backward compatibility

_add_annotation_value

  Title   : _add_annotation_value
  Usage   :
  Function: Adds a value to the annotation collection under the specified
            key. Note that this is not a public method.
  Returns : 
  Args    : key (a string), value(s) (one or more scalars)
 
 

_get_annotation_values

  Title   : _get_annotation_values
  Usage   :
  Function: Gets the values of a specific annotation as identified by the
            key from the annotation collection. Note that this is not a
            public method.
  Example :
  Returns : an array of strings
  Args    : the key (a string)