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), "\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_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