- Implemented Interfaces
- AUTHOR - Ewan Birney
- Private methods and synonyms for backward compatibility
Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry
See Bio::Seq::RichSeqI and documentation of methods.
This module implements 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 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
This class implementes the following interfaces.
Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI, specifically via Bio::Seq and Bio::PrimarySeq. Please review the documentation for those modules on implementation details relevant to those interfaces, as well as the ones below.
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@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $seq = 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 Bio::Seq::RichSeq object
Title : division Usage : $obj->division($newval) Function: Returns : value of division Args : newvalue (optional)
Title : molecule Usage : $obj->molecule($newval) Function: Returns : type of molecule (DNA, mRNA) Args : newvalue (optional)
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 strings
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 :
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 :
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)
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 strings
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 : none
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 Bio::PrimarySeq version() in that this explicitly refers to the sequence record version one would find in a typical sequence file.
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)
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 :
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)
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)