bio::seqio::locuslink(3pm) [debian man page]
Bio::SeqIO::locuslink(3pm) User Contributed Perl Documentation Bio::SeqIO::locuslink(3pm) 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://redmine.open-bio.org/projects/bioperl/ 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 _ perl v5.14.2 2012-03-02 Bio::SeqIO::locuslink(3pm)
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Bio::AnnotatableI(3pm) User Contributed Perl Documentation Bio::AnnotatableI(3pm) NAME
Bio::AnnotatableI - the base interface an annotatable object must implement SYNOPSIS
use Bio::SeqIO; # get an annotatable object somehow: for example, Bio::SeqI objects # are annotatable my $seqio = Bio::SeqIO->new(-fh => *STDIN, -format => 'genbank'); while (my $seq = $seqio->next_seq()) { # $seq is-a Bio::AnnotatableI, hence: my $ann_coll = $seq->annotation(); # $ann_coll is-a Bio::AnnotationCollectionI, hence: my @all_anns = $ann_coll->get_Annotations(); # do something with the annotation objects } DESCRIPTION
This is the base interface that all annotatable objects must implement. A good example is Bio::Seq which is an AnnotableI object. 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://redmine.open-bio.org/projects/bioperl/ AUTHOR
Hilmar Lapp E<lt>hlapp@gmx.netE<gt> Allen Day E<lt>allenday@ucla.eduE<gt> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ annotation Title : annotation Usage : $obj->annotation($newval) Function: Get the annotation collection for this annotatable object. Example : Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : on set, new value (a Bio::AnnotationCollectionI implementing object, optional) (an implementation may not support changing the annotation collection) See Bio::AnnotationCollectionI perl v5.14.2 2012-03-02 Bio::AnnotatableI(3pm)