Christopher Fields > BioPerl > Bio::SeqIO::locuslink



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Module Version: 1.006924   Source  


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.


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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.

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AUTHOR - Keith Ching ^

Email kching at


Hilmar Lapp, hlapp at


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

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