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
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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 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 :