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). For a general implementation, please see the documentation for Bio::Seq::RichSeq.

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:

https://redmine.open-bio.org/projects/bioperl/

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    :
Note    : this differs from Bio::PrimarySeq version() in that this explicitly
          refers to the sequence record version one would find in a typical
          sequence file.  It is up to the implementation whether this is set
          separately or falls back to the more generic Bio::Seq::version()

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    : 

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq