/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::embl

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)