Bio::SeqIO::embl(3)

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://github.com/bioperl/bioperl-live/issues

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)