Bio::SeqIO::embl - EMBL sequence input/output stream It is probably best not to use this object directly, but rather go through the AnnSeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL'); while ( (my $seq = $stream->next_seq()) ) { # do something with $seq } This object can transform Bio::Seq objects to and from EMBL flat file databases. There is alot of flexibility here about how to dump things which I need to document fully. There should be a common object that this and genbank share (probably with swissprot). Too much of the magic is identical.

Optional functions
(output only) shows the dna or not (output only) provides a sorting func which is applied to the FTHelpers before printing This is function which is called as print "ID ", $func($annseq), "\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 embl 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 polled from a Bio::Annotation::Collection object. reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain Bio::Annotation::DBLink objects

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://www.bioperl.org/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email birney@ebi.ac.uk Describe contact details here 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_EMBL_FTHelper
Title : _print_EMBL_FTHelper Usage : Function: Internal function Returns : Args :

_read_EMBL_Species
Title : _read_EMBL_Species Usage : Function: Reads the EMBL Organism species and classification lines. Example : Returns : A Bio::Species object Args : a reference to the current line buffer

_read_EMBL_DBLink
Title : _read_EMBL_DBLink Usage : Function: Reads the EMBL database cross reference ("DR") lines Example : Returns : A list of Bio::Annotation::DBLink objects Args :

_filehandle
Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)

_read_FTHelper_EMBL
Title : _read_FTHelper_EMBL Usage : _read_FTHelper_EMBL($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar

_write_line_EMBL
Title : _write_line_EMBL Usage : Function: internal function Example : Returns : Args :

_write_line_EMBL_regex
Title : _write_line_EMBL_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)