- AUTHOR - Keith Ching
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 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.
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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 _