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 : $@\n"; }
This module seeks to provide a simple method for pushing sequence changes back to a Sequence Database - which can be an SQL compliant database, a file based database, AceDB, etc.
Jason Stajich <jason@bioperl.org>
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : write_seq Usage : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs) Function: updates sequences in first array, adds sequences in the second array, and removes sequences in the third array. Example : Returns : Args : arrays of sequence objects that must be obtained from Bio::DB::UpdateableSeqI.
Title : _add_seq Usage : _add_seq($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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.