Manual Reference Pages - BIO::SEQIO::LOCUSLINK (3)
Bio::SeqIO::locuslink - LocusLink input/output stream
# dont 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 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.
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.
firstname.lastname@example.org - 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
AUTHOR - Keith Ching
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 _
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