| Bio::Seq::RichSeqI(3pm) | User Contributed Perl Documentation | Bio::Seq::RichSeqI(3pm) |
Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
@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;
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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 :
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 :
Title : pid
Usage :
Function: Get (and set, depending on the implementation) the PID property
for the sequence.
Example :
Returns : a string
Args :
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 :
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()
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 :
| 2021-08-15 | perl v5.32.1 |