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