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Man Pages


Manual Reference Pages  -  BIO::SEQIO::EMBL (3)

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NAME

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

CONTENTS

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)



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