Reference

Bio::Seq::RichSeqI(3pm)

interface for sequences from rich data sources, mostly databases

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email [email protected]

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 division 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    :

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