| Bio::DB::UpdateableSeqI(3pm) | User Contributed Perl Documentation | Bio::DB::UpdateableSeqI(3pm) |
Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
# get a Bio::DB::UpdateableSeqI somehow
eval {
my ( @updatedseqs, @newseqs, @deadseqs);
my $seq = $db->get_Seq_by_id('ROA1_HUMAN');
$seq->desc('a new description');
push @updatedseqs, $seq;
$db->write_seq(\@updatedseqs, \@newseqs, \@deadseqs);
};
if( $@ ) {
print STDERR "an error when trying to write seq : $@\n";
}
This module seeks to provide a simple method for pushing sequence changes back to a Sequence Database - which can be an SQL compliant database, a file based database, AceDB, etc.
Jason Stajich <jason@bioperl.org>
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : write_seq
Usage : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs)
Function: updates sequences in first array,
adds sequences in the second array,
and removes sequences in the third array.
Example :
Returns :
Args : arrays of sequence objects that must be obtained from
Bio::DB::UpdateableSeqI.
Title : _add_seq
Usage : _add_seq($seq)
Function: Adds a new sequence
Example :
Returns : will throw an exception if
sequences accession number already exists
Args : a new seq object - should have an accession number
Title : _remove_seq
Usage : _remove_seq($seq)
Function: Removes an existing sequence
Example :
Returns : will throw an exception if
sequence does not exists for the primary_id
Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI
Title : _update_seq
Usage : _update_seq($seq)
Function: Updates a sequence
Example :
Returns : will throw an exception if
sequence is out of sync from expected val.
Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI
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_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
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
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
| 2018-10-27 | perl v5.26.2 |