Bio::SeqIO::locuslink - LocusLink input/output stream
# don't instantiate directly - instead do
my $seqio = Bio::SeqIO->new(-format => "locuslink", -file => \STDIN);
This module parses LocusLink into Bio::SeqI objects with rich annotation, but no
The input file has to be in the LL_tmpl format - the tabular format will not
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.
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.
email@example.com - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Email kching at gnf.org
Hilmar Lapp, hlapp at gmx.net
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _