plucky (3) Bio::SeqIO::locuslink.3pm.gz

Provided by: libbio-perl-perl_1.7.8-1_all bug

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 _