Bio::DB::SeqI(3) 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. 

  [email protected]                  - General discussion
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Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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

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