Bio::SeqIO::embldriver(3pm) User Contributed Perl Documentation Bio::SeqIO::embldriver(3pm)
NAME
Bio::SeqIO::embldriver - 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 => 'embldriver');
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), "
";
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://redmine.open-bio.org/projects/bioperl/
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_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 0 for error
Args : array of 1 to n Bio::SeqI objects
seqhandler
Title : seqhandler
Usage : $stream->seqhandler($handler)
Function: Get/Set teh Bio::Seq::HandlerBaseI object
Returns : Bio::Seq::HandlerBaseI
Args : Bio::Seq::HandlerBaseI
perl v5.14.2 2012-03-02 Bio::SeqIO::embldriver(3pm)