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Bio::SeqIO::embl.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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_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)