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::SeqIO::ace(3pm) User Contributed Perl Documentation Bio::SeqIO::ace(3pm) NAME
Bio::SeqIO::ace - ace sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION
This object can transform Bio::Seq objects to and from ace file format. It only parses a DNA or Peptide objects contained in the ace file, producing PrimarySeq objects from them. All other objects in the files will be ignored. It doesn't attempt to parse any annotation attatched to the containing Sequence or Protein objects, which would probably be impossible, since everyone's ACeDB schema can be different. It won't parse ace files containing Timestamps correctly either. This can easily be added if considered necessary. 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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHORS - James Gilbert Email: jgrg@sanger.ac.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object(s) perl v5.14.2 2012-03-02 Bio::SeqIO::ace(3pm)