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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)

Check Out this Related Man Page

Bio::SeqIO::pir(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::pir(3pm)

NAME

       Bio::SeqIO::pir - PIR 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 pir flat file databases.

       Note: This does not completely preserve the PIR format - quality information about sequence is currently discarded since bioperl does not
       have a mechanism for handling these encodings in sequence data.

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

       Aaron Mackey <amackey@virginia.edu> Lincoln Stein <lstein@cshl.org> Jason Stajich <jason@bioperl.org>

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	: Array of Bio::PrimarySeqI objects

perl v5.14.2							    2012-03-02						      Bio::SeqIO::pir(3pm)
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