| Bio::DB::SeqI(3pm) | User Contributed Perl Documentation | Bio::DB::SeqI(3pm) |
Bio::DB::SeqI - Abstract Interface for Sequence databases
# 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
}
Abstract interface for a sequence database
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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
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
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
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
| 2021-08-15 | perl v5.32.1 |