Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::SeqIO::embl - EMBL sequence input/output stream

SYNOPSIS

       It is probably best not to use this object directly, but rather go through the SeqIO
       handler system. Go:

           $stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL');

           while ( (my $seq = $stream->next_seq()) ) {
               # do something with $seq
           }

DESCRIPTION

       This object can transform Bio::Seq objects to and from EMBL flat file databases.

       There is a lot of flexibility here about how to dump things which should be documented
       more fully.

       There should be a common object that this and Genbank share (probably with Swissprot). Too
       much of the magic is identical.

   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   ", $func($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

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney

       Email birney@ebi.ac.uk

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_ID_line
        Title   : _write_ID_line
        Usage   : $self->_write_ID_line($seq);
        Function: Writes the EMBL Release 87 format ID line to the stream, unless
                : there is a user-supplied ID line generation function in which
                : case that is used instead.
                : ( See Bio::SeqIO::embl::_id_generation_function(). )
        Returns : nothing
        Args    : Bio::Seq object

   _is_valid_division
        Title   : _is_valid_division
        Usage   : $self->_is_valid_division($div)
        Function: tests division code for validity
        Returns : true if $div is a valid EMBL release 87 taxonomic division.
        Args    : taxonomic division code string

   _is_valid_molecule_type
        Title   : _is_valid_molecule_type
        Usage   : $self->_is_valid_molecule_type($mol)
        Function: tests molecule type for validity
        Returns : true if $mol is a valid EMBL release 87 molecule type.
        Args    : molecule type string

   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 undef for error
        Args    : array of 1 to n Bio::SeqI objects

   _print_EMBL_FTHelper
        Title   : _print_EMBL_FTHelper
        Usage   :
        Function: Internal function
        Returns : 1 if writing suceeded, otherwise undef
        Args    :

   _read_EMBL_Contig()
        Title   : _read_EMBL_Contig
        Usage   :
        Function: convert CO lines into annotations
        Returns :
        Args    :

   _read_EMBL_References
        Title   : _read_EMBL_References
        Usage   :
        Function: Reads references from EMBL format. Internal function really
        Example :
        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, accession number

   _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    :

   _read_EMBL_TaxID_DBLink
        Title   : _read_EMBL_TaxID_DBLink
        Usage   :
        Function: Reads the EMBL database cross reference to NCBI TaxID ("OX") 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 : 1 if writing suceeded, else undef
        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)