Bio::Assembly::ContigAnalysis(3pm)			User Contributed Perl Documentation			Bio::Assembly::ContigAnalysis(3pm)

NAME

       Bio::Assembly::ContigAnalysis -
	   Perform analysis on sequence assembly contigs.

SYNOPSIS

	   # Module loading
	   use Bio::Assembly::ContigAnalysis;

	   # Assembly loading methods
	   my $ca = Bio::Assembly::ContigAnalysis->new( -contig=>$contigOBJ );

	   my @lcq = $ca->low_consensus_quality;
	   my @hqd = $ca->high_quality_discrepancies;
	   my @ss  = $ca->single_strand_regions;

DESCRIPTION

       A contig is as a set of sequences, locally aligned to each other, when the sequences in a pair may be aligned. It may also include a
       consensus sequence. Bio::Assembly::ContigAnalysis is a module holding a collection of methods to analyze contig objects. It was developed
       around the Bio::Assembly::Contig implementation of contigs and can not work with another contig interface.

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 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 - Robson Francisco de Souza
       Email: rfsouza@citri.iq.usp.br

APPENDIX

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

Object creator
   new
	Title	  : new
	Usage	  : my $contig = Bio::Assembly::ContigAnalysis->new(-contig=>$contigOBJ);
	Function  : Creates a new contig analysis object
	Returns   : Bio::Assembly::ContigAnalysis
	Args	  :
		    -contig : a Bio::Assembly::Contig object

Analysis methods
   high_quality_discrepancies
	Title	  : high_quality_discrepancies
	Usage	  : my $sfc = $ContigAnal->high_quality_discrepancies();
	Function  :

		    Locates all high quality discrepancies among aligned
		    sequences and the consensus sequence.

		    Note: see Bio::Assembly::Contig POD documentation,
		    section "Coordinate System", for a definition of
		    available types. Default coordinate system type is
		    "gapped consensus", i.e. consensus sequence (with gaps)
		    coordinates. If limits are not specified, the entire
		    alignment is analyzed.

	Returns   : Bio::SeqFeature::Collection
	Args	  : optional arguments are
		    -threshold : cutoff value for low quality (minimum high quality)
				 Default: 40
		    -ignore    : number of bases that will not be analysed at
				 both ends of contig aligned elements
				 Default: 5
		    -start     : start of interval that will be analyzed
		    -end       : start of interval that will be analyzed
		    -type      : coordinate system type for interval

   low_consensus_quality
	Title	  : low_consensus_quality
	Usage	  : my $sfc = $ContigAnal->low_consensus_quality();
	Function  : Locates all low quality regions in the consensus
	Returns   : an array of Bio::SeqFeature::Generic objects
	Args	  : optional arguments are
		    -threshold : cutoff value for low quality (minimum high quality)
				 Default: 25
		    -start     : start of interval that will be analyzed
		    -end       : start of interval that will be analyzed
		    -type      : coordinate system type for interval

   not_confirmed_on_both_strands
	Title	  : low_quality_consensus
	Usage	  : my $sfc = $ContigAnal->low_quality_consensus();
	Function  :

		    Locates all regions whose consensus bases were not
		    confirmed by bases from sequences aligned in both
		    orientations, i.e., in such regions, no bases in aligned
		    sequences of either +1 or -1 strand agree with the
		    consensus bases.

	Returns   : an array of Bio::SeqFeature::Generic objects
	Args	  : optional arguments are
		    -start : start of interval that will be analyzed
		    -end   : start of interval that will be analyzed
		    -type  : coordinate system type for interval

   single_strand
	Title	  : single_strand
	Usage	  : my $sfc = $ContigAnal->single_strand();
	Function  :

		    Locates all regions covered by aligned sequences only in
		    one of the two strands, i.e., regions for which aligned
		    sequence's strand() method returns +1 or -1 for all
		    sequences.

	Returns   : an array of Bio::SeqFeature::Generic objects
	Args	  : optional arguments are
		    -start : start of interval that will be analyzed
		    -end   : start of interval that will be analyzed
		    -type  : coordinate system type for interval

Internal Methods
   _merge_overlapping_features
	Title	  : _merge_overlapping_features
	Usage	  : my @feat = $ContigAnal->_merge_overlapping_features(@features);
	Function  : Merge all overlapping features into features
		    that hold original features as sub-features
	Returns   : array of Bio::SeqFeature::Generic objects
	Args	  : array of Bio::SeqFeature::Generic objects

   _complementary_features_list
	Title	  : _complementary_features_list
	Usage	  : @feat = $ContigAnal->_complementary_features_list($start,$end,@features);
	Function  : Build a list of features for regions
		    not covered by features in @features array
	Returns   : array of Bio::SeqFeature::Generic objects
	Args	  :
		    $start    : [integer] start of first output feature
		    $end      : [integer] end of last output feature
		    @features : array of Bio::SeqFeature::Generic objects

perl v5.14.2							    2012-03-02					Bio::Assembly::ContigAnalysis(3pm)