Bio::Seq::RichSeqI(3pm) User Contributed Perl Documentation Bio::Seq::RichSeqI(3pm)
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 :
perl v5.14.2 2012-03-02 Bio::Seq::RichSeqI(3pm)