Bio::Seq::RichSeqI.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases

SYNOPSIS

     @secondary   = $richseq->get_secondary_accessions;
     $division    = $richseq->division;
     $mol         = $richseq->molecule;
     @dates       = $richseq->get_dates;
     $seq_version = $richseq->seq_version;
     $pid         = $richseq->pid;
     @keywords    = $richseq->get_keywords;
 
 

DESCRIPTION

This interface extends the Bio::SeqI interface to give additional functionality to sequences with richer data sources, in particular from database sequences (EMBL, GenBank and Swissprot).

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 _

get_secondary_accessions

  Title   : get_secondary_accessions
  Usage   : 
  Function: Get the secondary accessions for a sequence.
 
            An implementation that allows modification of this array
            property should provide the methods add_secondary_accession
            and remove_secondary_accessions, with obvious purpose.
 
  Example :
  Returns : an array of strings
  Args    : none
 
 

division

  Title   : division
  Usage   :
  Function: Get (and set, depending on the implementation) the divison for
            a sequence.
 
            Examples from GenBank are PLN (plants), PRI (primates), etc.
  Example :
  Returns : a string
  Args    :
 
 

molecule

  Title   : molecule
  Usage   :
  Function: Get (and set, depending on the implementation) the molecule
            type for the sequence.
 
            This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
            because it is databank-specific.
  Example :
  Returns : a string
  Args    :
 
 

pid

  Title   : pid
  Usage   :
  Function: Get (and set, depending on the implementation) the PID property
            for the sequence.
  Example :
  Returns : a string
  Args    :
 
 

get_dates

  Title   : get_dates
  Usage   :
  Function: Get (and set, depending on the implementation) the dates the
            databank entry specified for the sequence
 
            An implementation that allows modification of this array
            property should provide the methods add_date and
            remove_dates, with obvious purpose.
 
  Example :
  Returns : an array of strings
  Args    :
 
 

seq_version

  Title   : seq_version
  Usage   :
  Function: Get (and set, depending on the implementation) the version string
            of the sequence.
  Example :
  Returns : a string
  Args    :
 
 

get_keywords

  Title   : get_keywords
  Usage   : $obj->get_keywords()
  Function: Get the keywords for this sequence object.
 
            An implementation that allows modification of this array
            property should provide the methods add_keyword and
            remove_keywords, with obvious purpose.
 
  Returns : an array of strings
  Args    :