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.

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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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email birney@ebi.ac.uk Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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

division
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 a date Example : Returns : a date string or an array of such strings Args :

get_dates
Title : get_dates Usage : Function: Example : Returns : an array of date strings Args :

pid
Title : pid Usage : Function: Get (and set, depending on the implementation) the PID property for the sequence. Example : 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 Example : Returns : Args : a string or an array of strings

get_secondary_accessions
Title : get_secondary_accessions Usage : Function: Example : Returns : An array of strings Args :

seq_version
Title : seq_version Usage : $obj->seq_version($newval) Function: Example : Returns : value of seq_version Args : newvalue (optional)

keywords
Title : keywords Usage : $obj->keywords($newval) Function: Returns : value of keywords (a string) Args : newvalue (optional) (a string)