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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::locuslink 3pm"
.TH Bio::SeqIO::locuslink 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SeqIO::locuslink \- LocusLink input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&   # don\*(Aqt instantiate directly \- instead do
\&   my $seqio = Bio::SeqIO\->new(\-format => "locuslink", \-file => \eSTDIN);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module parses LocusLink into Bio::SeqI objects with rich
annotation, but no sequence.
.PP
The input file has to be in the LL_tmpl format \- the tabular format
will not work.
.PP
The way the current implementation populates the object is rather a
draft work than a finished work of art. Note that at this stage the
LocusLink entries cannot be round-tripped, because the parser loses
certain information. For instance, most of the alternative transcript
descriptions are not retained. The parser also misses any element
that deals with visual representation (e.g., 'button') except for the
URLs. Almost all of the pieces of the annotation are kept in a
Bio::Annotation::Collection object, see Bio::Annotation::Collection
for more information.
.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
the Bioperl mailing list.  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
of 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 \- Keith Ching"
.IX Header "AUTHOR - Keith Ching"
Email kching at gnf.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Hilmar Lapp, hlapp at gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _