/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::DB::SeqI

NAME

Bio::DB::SeqI - Abstract Interface for Sequence databases

SYNOPSIS

# get a Bio::DB::SeqI somehow

$seq = $seqdb->get_Seq_by_id('some-id');
$seq = $seqdb->get_Seq_by_acc('some-accession-number');

@ids = $seqdb->get_all_ids();
$stream = $seqdb->get_PrimarySeq_stream();
while((my $seq = $stream->next_seq()) {
   # $seq is a PrimarySeqI compliant object
}

DESCRIPTION

Abstract interface for a sequence database

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@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

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

get_Seq_by_version

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

Methods [that were] specific for Bio::DB::SeqI

get_PrimarySeq_stream

Title   : get_PrimarySeq_stream
Usage   : $stream = get_PrimarySeq_stream
Function: Makes a Bio::SeqIO compliant object
          which provides a single method, next_seq
Returns : Bio::SeqIO
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
          may be 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