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Bio::SeqIO::embl(3)   User Contributed Perl Documentation  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:

	 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)

perl v5.14.1			  2011-07-22		   Bio::SeqIO::embl(3)
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