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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::embldriver 3pm"
.TH Bio::SeqIO::embldriver 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::SeqIO::embldriver \- EMBL sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
It is probably best not to use this object directly, but
rather go through the SeqIO handler system. Go:
.PP
.Vb 1
\&    $stream = Bio::SeqIO\->new(\-file => $filename, \-format => \*(Aqembldriver\*(Aq);
\&
\&    while ( (my $seq = $stream\->next_seq()) ) {
\&        # do something with $seq
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Seq objects to and from \s-1EMBL\s0 flat
file databases.
.PP
There is a lot of flexibility here about how to dump things which
should be documented more fully.
.PP
There should be a common object that this and Genbank share (probably
with Swissprot). Too much of the magic is identical.
.SS "Optional functions"
.IX Subsection "Optional functions"
.IP "\fB_show_dna()\fR" 3
.IX Item "_show_dna()"
(output only) shows the dna or not
.IP "\fB_post_sort()\fR" 3
.IX Item "_post_sort()"
(output only) provides a sorting func which is applied to the FTHelpers
before printing
.IP "\fB_id_generation_func()\fR" 3
.IX Item "_id_generation_func()"
This is function which is called as
.Sp
.Vb 1
\&   print "ID   ", $func($annseq), "\en";
.Ve
.Sp
To generate the \s-1ID\s0 line. If it is not there, it generates a sensible \s-1ID\s0
line using a number of tools.
.Sp
If you want to output annotations in \s-1EMBL\s0 format they need to be
stored in a Bio::Annotation::Collection object which is accessible
through the Bio::SeqI interface method \fBannotation()\fR.
.Sp
The following are the names of the keys which are polled from a
Bio::Annotation::Collection object.
.Sp
.Vb 3
\& reference  \- Should contain Bio::Annotation::Reference objects
\& comment    \- Should contain Bio::Annotation::Comment objects
\& dblink     \- Should contain Bio::Annotation::DBLink objects
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Ewan Birney"
.IX Header "AUTHOR - Ewan Birney"
Email birney@ebi.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $seq = $stream\->next_seq()
\& Function: returns the next sequence in the stream
\& Returns : Bio::Seq object
\& Args    :
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& 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
.Ve
.SS "seqhandler"
.IX Subsection "seqhandler"
.Vb 5
\& Title   : seqhandler
\& Usage   : $stream\->seqhandler($handler)
\& Function: Get/Set the Bio::Seq::HandlerBaseI object
\& Returns : Bio::Seq::HandlerBaseI 
\& Args    : Bio::Seq::HandlerBaseI
.Ve