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bio::coordinate::utils(3pm) [debian man page]

Bio::Coordinate::Utils(3pm)				User Contributed Perl Documentation			       Bio::Coordinate::Utils(3pm)

NAME

       Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects

SYNOPSIS

	   use Bio::Coordinate::Utils;
	   # get a Bio::Align::AlignI compliant object, $aln, somehow
	   # it could be a Bio::SimpleAlign

	   $mapper = Bio::Coordinate::Utils->from_align($aln, 1);

	   # Build a set of mappers which will map, for each sequence,
	   # that sequence position in the alignment (exon position to alignment
	   # position)
	   my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);

DESCRIPTION

       This class is a holder of methods that work on or create Bio::Coordinate::MapperI- compliant objects. . These methods are not part of the
       Bio::Coordinate::MapperI interface and should in general not be essential to the primary function of sequence objects. If you are thinking
       of adding essential functions, it might be better to create your own sequence class.  See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq
       for more.

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/

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

       Jason Stajich jason at bioperl.org

APPENDIX

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

   from_align
	Title	: from_align
	Usage	: $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
	Function:
		  Create a mapper out of an alignment.
		  The mapper will return a value only when both ends of
		  the input range find a match.

		  Note: This implementation works only on pairwise alignments
		  and is not yet well tested!

	Returns : A Bio::Coordinate::MapperI
	Args	: Bio::Align::AlignI object
		  Id for the reference sequence, optional

   from_seq_to_alignmentpos
	Title	: from_seq_to_alignmentpos
	Usage	: $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
	Function:
		  Create a mapper out of an alignment.
		  The mapper will map the position of a sequence into that position
		  in the alignment.

		  Will work on alignments of >= 2 sequences
	Returns : An array of Bio::Coordinate::MapperI
	Args	: Bio::Align::AlignI object

perl v5.14.2							    2012-03-02					       Bio::Coordinate::Utils(3pm)

Check Out this Related Man Page

Bio::AlignIO::emboss(3pm)				User Contributed Perl Documentation				 Bio::AlignIO::emboss(3pm)

NAME

       Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)

SYNOPSIS

	   # do not use the object directly
	   use Bio::AlignIO;
	   # read in an alignment from the EMBOSS program water
	   my $in = Bio::AlignIO->new(-format => 'emboss',
				     -file   => 'seq.water');
	   while( my $aln = $in->next_aln ) {
	   # do something with the alignment
	   }

DESCRIPTION

       This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.

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 - Jason Stajich
       Email jason@bioperl.org

APPENDIX

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

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln()
	Function: returns the next alignment in the stream.
	Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
		   or on error
	Args	: NONE

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the $aln object into the stream in emboss format
	Returns : 1 for success and 0 for error
	Args	: L<Bio::Align::AlignI> object

perl v5.14.2							    2012-03-02						 Bio::AlignIO::emboss(3pm)
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