Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
Bio::SeqIO::embldriverUser Contributed Perl DocumentaBio::SeqIO::embldriver(3)

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

       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 => 'embldriver');

	   while ( (my $seq = $stream->next_seq()) ) {
	       # do something with $seq

       This object can transform Bio::Seq objects to and from EMBL flat	file

       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
	  (output only)	shows the dna or not

	  (output only)	provides a sorting func	which is applied to the
	  FTHelpers before printing

	  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

   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.			- General discussion	- About	the mailing lists

       Please direct usage questions or	support	issues to the mailing list:

       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

AUTHOR - Ewan Birney

       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns	: Bio::Seq object
	Args	:

	Title	: write_seq
	Usage	: $stream->write_seq($seq)
	Function: writes the $seq object (must be seq) to the stream
	Returns	: 1 for	success	and 0 for error
	Args	: array	of 1 to	n Bio::SeqI objects

	Title	: seqhandler
	Usage	: $stream->seqhandler($handler)
	Function: Get/Set the Bio::Seq::HandlerBaseI object
	Returns	: Bio::Seq::HandlerBaseI
	Args	: Bio::Seq::HandlerBaseI

perl v5.32.1			  2019-12-07	     Bio::SeqIO::embldriver(3)


Want to link to this manual page? Use this URL:

home | help