NAME
FAST::Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry
SYNOPSIS
See FAST::Bio::Seq::RichSeqI and documentation of methods.
DESCRIPTION
This module implements FAST::Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the FAST::Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided.
For more information, please see the relevant
Implemented Interfaces
This class implementes the following interfaces.
- FAST::Bio::Seq::RichSeqI
-
Note that this includes implementing FAST::Bio::PrimarySeqI and FAST::Bio::SeqI, specifically via FAST::Bio::Seq and FAST::Bio::PrimarySeq. Please review the documentation for those modules on implementation details relevant to those interfaces, as well as the ones below.
- FAST::Bio::IdentifiableI
- FAST::Bio::DescribableI
- FAST::Bio::AnnotatableI
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 listsSupport
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 _
new
Title : new
Usage : $seq = FAST::Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
-id => 'human_id',
-accession_number => 'AL000012',
);
Function: Returns a new seq object from
basic constructors, being a string for the sequence
and strings for id and accession_number
Returns : a new FAST::Bio::Seq::RichSeq objectdivision
Title : division
Usage : $obj->division($newval)
Function:
Returns : value of division
Args : newvalue (optional)molecule
Title : molecule
Usage : $obj->molecule($newval)
Function:
Returns : type of molecule (DNA, mRNA)
Args : newvalue (optional)add_date
Title : add_date
Usage : $self->add_date($datestr)
Function: adds one or more dates
This implementation stores dates as keyed annotation, the
key being 'date_changed'. You can take advantage of this
fact when accessing the annotation collection directly.
Example :
Returns :
Args : a date string or an array of such stringsget_dates
Title : get_dates
Usage : my @dates = $seq->get_dates;
Function: Get the dates of the sequence (usually, when it was created and
changed.
Returns : an array of date strings
Args :pid
Title : pid
Usage : my $pid = $seq->pid();
Function: Get (and set, depending on the implementation) the PID property
for the sequence.
Returns : a string
Args :accession
Title : accession
Usage : $obj->accession($newval)
Function: Whilst the underlying sequence object does not
have an accession, so we need one here.
In this implementation this is merely a synonym for
accession_number().
Example :
Returns : value of accession
Args : newvalue (optional)add_secondary_accession
Title : add_secondary_accession
Usage : $self->add_domment($ref)
Function: adds a secondary_accession
This implementation stores secondary accession numbers as
keyed annotation, the key being 'secondary_accession'. You
can take advantage of this fact when accessing the
annotation collection directly.
Example :
Returns :
Args : a string or an array of stringsget_secondary_accessions
Title : get_secondary_accessions
Usage : my @acc = $seq->get_secondary_accessions();
Function: Get the secondary accession numbers as strings.
Returns : An array of strings
Args : noneseq_version
Title : seq_version
Usage : $obj->seq_version($newval)
Function: Get/set the sequence version
Returns : value of seq_version (a scalar)
Args : on set, new value (a scalar or undef, optional)
Note : this differs from FAST::Bio::PrimarySeq version() in that this explicitly
refers to the sequence record version one would find in a typical
sequence file. add_keyword
Title : add_keyword
Usage : $obj->add_keyword($newval)
Function: Add a new keyword to the annotation of the sequence.
This implementation stores keywords as keyed annotation,
the key being 'keyword'. You can take advantage of this
fact when accessing the annotation collection directly.
Returns :
Args : value to be added (optional) (a string)get_keywords
Title : get_keywords
Usage : $obj->get_keywords($newval)
Function: Get the keywords for this sequence as an array of strings.
Returns : an array of strings
Args : Private methods and synonyms for backward compatibility
_add_annotation_value
Title : _add_annotation_value
Usage :
Function: Adds a value to the annotation collection under the specified
key. Note that this is not a public method.
Returns :
Args : key (a string), value(s) (one or more scalars)_get_annotation_values
Title : _get_annotation_values
Usage :
Function: Gets the values of a specific annotation as identified by the
key from the annotation collection. Note that this is not a
public method.
Example :
Returns : an array of strings
Args : the key (a string)