Bio::DB::BioSeqI - Abstract interface for a sequence database
# # get a database object somehow using a concrete class # $seq = $db->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object #
This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement.
The Bio::DB::BioSeqI class defines what methods a generic database class should have. At the moment it is just the ability to make Bio::Seq objects from a name (id) or a accession number.
Ewan Birney originally wrote this class.
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/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.