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Bio::SeqIO::locuslink(User Contributed Perl DocumentatBio::SeqIO::locuslink(3)

NAME
       Bio::SeqIO::locuslink - LocusLink input/output stream

SYNOPSIS
	  # don't instantiate directly - instead do
	  my $seqio = Bio::SeqIO->new(-format => "locuslink", -file => \STDIN);

DESCRIPTION
       This module parses LocusLink into Bio::SeqI objects with	rich
       annotation, but no sequence.

       The input file has to be	in the LL_tmpl format -	the tabular format
       will not	work.

       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.

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 the
       Bioperl mailing list.  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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Keith Ching
       Email kching at gnf.org

CONTRIBUTORS
       Hilmar Lapp, hlapp at gmx.net

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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Keith Ching | CONTRIBUTORS | APPENDIX

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