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15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
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- License: perl_5
- Perl: v5.6.1
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- NAME
- SYNOPSIS
- DESCRIPTION
- FEEDBACK
- AUTHOR - Ewan Birney
- APPENDIX
- Methods inherited from Bio::DB::RandomAccessI
- Methods [that were] specific for Bio::DB::SeqI
NAME
Bio::DB::CacheServer::SeqDB - Caching DB object
SYNOPSIS
Give standard usage here
DESCRIPTION
Bio::DB::SeqI implmenting object which implements a cache via a bioperl-db database handle
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@bio.perl.org
Support
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:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
Describe contact details here
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Methods inherited from Bio::DB::RandomAccessI
get_Seq_by_id
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
get_Seq_by_acc
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
Methods [that were] specific for Bio::DB::SeqI
get_PrimarySeq_stream
Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq Returns : Bio::DB::SeqStreamI Args : none
get_all_primary_ids
Title : get_all_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none
get_Seq_by_primary_id
Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception
Get/Sets for attributes stored in this object
seq_adaptor
Title : seq_adaptor Usage : $obj->seq_adaptor($newval) Function: Example : Returns : value of seq_adaptor Args : newvalue (optional)
db_adaptor
Title : db_adaptor Usage : $obj->db_adaptor($newval) Function: Example : Returns : value of db_adaptor Args : newvalue (optional)
dbid
Title : dbid Usage : $obj->dbid($newval) Function: Example : Returns : value of dbid Args : newvalue (optional)
read_db
Title : read_db Usage : $obj->read_db($newval) Function: Example : Returns : value of read_db Args : newvalue (optional)
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
cpanm Bio::BioEntry
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.