Bio::DB::InMemoryCache - Abstract interface for a sequence database
$cachedb = Bio::DB::InMemoryCache->new( -seqdb => $real_db, -number => 1000); # # get a database object somehow using a concrete class # $seq = $cachedb->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object #
This is a memory cache system which saves the objects returned by Bio::DB::RandomAccessI in memory to a hard limit of sequences.
Ewan Birney <birney@ebi.ac.uk>
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:
http://bugzilla.open-bio.org/
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
Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version 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.