--- name: "Bio::SeqIO::genbank" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::SeqIO::genbank" --- # Bio::SeqIO::genbank(3pm) GenBank sequence input/output stream ## NAME Bio::SeqIO::genbank - GenBank sequence input/output stream ## SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler: ``` $stream = Bio::SeqIO->new(-file => $filename, -format => 'GenBank'); while ( my $seq = $stream->next_seq ) { # do something with $seq } ``` ## DESCRIPTION This object can transform Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. ### Optional functions - **\_show\_dna()** (output only) shows the dna or not - **\_post\_sort()** (output only) provides a sorting func which is applied to the FTHelpers before printing - **\_id\_generation\_func()** This is function which is called as ``` print "ID ", $func($seq), "\n"; ``` To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. If you want to output annotations in Genbank format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method **annotation()**. The following are the names of the keys which are pulled from a Bio::Annotation::Collection object: ``` reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain a Bio::Annotation::DBLink object segment - Should contain a Bio::Annotation::SimpleValue object origin - Should contain a Bio::Annotation::SimpleValue object wgs - Should contain a Bio::Annotation::SimpleValue object ``` ## Where does the data go? Data parsed in Bio::SeqIO::genbank is stored in a variety of data fields in the sequence object that is returned. Here is a partial list of fields. Items listed as RichSeq or Seq or PrimarySeq and then **NAME()** tell you the top level object which defines a function called **NAME()** which stores this information. Items listed as Annotation 'NAME' tell you the data is stored the associated Bio::AnnotationCollectionI object which is associated with Bio::Seq objects. If it is explicitly requested that no annotations should be stored when parsing a record of course they will not be available when you try and get them. If you are having this problem look at the type of SeqBuilder that is being used to construct your sequence object. ``` Comments Annotation 'comment' References Annotation 'reference' Segment Annotation 'segment' Origin Annotation 'origin' Dbsource Annotation 'dblink' Accessions PrimarySeq accession_number() Secondary accessions RichSeq get_secondary_accessions() GI number PrimarySeq primary_id() LOCUS PrimarySeq display_id() Keywords RichSeq get_keywords() Dates RichSeq get_dates() Molecule RichSeq molecule() Seq Version RichSeq seq_version() PID RichSeq pid() Division RichSeq division() Features Seq get_SeqFeatures() Alphabet PrimarySeq alphabet() Definition PrimarySeq description() or desc() Version PrimarySeq version() Sequence PrimarySeq seq() ``` There is more information in the Feature-Annotation HOWTO about each field and how it is mapped to the Sequence object \. ## 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 - Bioperl Project bioperl-l at bioperl.org Original author Elia Stupka, elia -at- tigem.it ## CONTRIBUTORS Ewan Birney birney at ebi.ac.uk Jason Stajich jason at bioperl.org Chris Mungall cjm at fruitfly.bdgp.berkeley.edu Lincoln Stein lstein at cshl.org Heikki Lehvaslaiho, heikki at ebi.ac.uk Hilmar Lapp, hlapp at gmx.net Donald G. Jackson, donald.jackson at bms.com James Wasmuth, james.wasmuth at ed.ac.uk Brian Osborne, bosborne at alum.mit.edu Chris Fields, cjfields at bioperl dot org ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### next\_seq ``` Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : ``` ### write\_seq ``` Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects ``` ### \_print\_GenBank\_FTHelper ``` Title : _print_GenBank_FTHelper Usage : Function: Example : Returns : Args : ``` ### \_read\_GenBank\_References ``` Title : _read_GenBank_References Usage : Function: Reads references from GenBank format. Internal function really Returns : Args : ``` ### \_add\_ref\_to\_array Title: \_add\_ref\_to\_array Usage: Function: Adds a Reference object to an array of Reference objects, takes\ care of possible cleanups to be done (currently, only author and title\ will be chopped of trailing semicolons). Args: A reference to an array of Reference objects and\ the Reference object to be added Returns: nothing ### \_read\_GenBank\_Species ``` Title : _read_GenBank_Species Usage : Function: Reads the GenBank Organism species and classification lines. Able to deal with unconvential Organism naming formats, and varietas in plants Example : ORGANISM unknown marine gamma proteobacterium NOR5 $genus = undef $species = unknown marine gamma proteobacterium NOR5 ORGANISM Drosophila sp. 'white tip scutellum' $genus = Drosophila $species = sp. 'white tip scutellum' (yes, this really is a species and that is its name) $subspecies = undef ORGANISM Ajellomyces capsulatus var. farciminosus $genus = Ajellomyces $species = capsulatus $subspecies = var. farciminosus ORGANISM Hepatitis delta virus $genus = undef (though this virus has a genus in its lineage, we cannot know that without a database lookup) $species = Hepatitis delta virus Returns : A Bio::Species object Args : A reference to the current line buffer ``` ### \_read\_FTHelper\_GenBank ``` Title : _read_FTHelper_GenBank Usage : _read_FTHelper_GenBank($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar ``` ### \_write\_line\_GenBank ``` Title : _write_line_GenBank Usage : Function: internal function Example : Returns : Args : ``` ### \_write\_line\_GenBank\_regex ``` Title : _write_line_GenBank_regex Usage : Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text Example : Returns : nothing Args : file handle, first header, second header, text-line, regex for line breaks, total line length ``` ### \_post\_sort ``` Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional) ``` ### \_show\_dna ``` Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional) ``` ### \_id\_generation\_func ``` Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional) ``` ### \_ac\_generation\_func ``` Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional) ``` ### \_sv\_generation\_func ``` Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional) ``` ### \_kw\_generation\_func ``` Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional) ```