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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Robson Francisco de Souza

Email: [email protected]

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