Bio::Assembly::ContigAnalysis - Perform analysis on sequence assembly contigs. # Module loading use Bio::Assembly::ContigAnalysis; # Assembly loading methods my $ca = new Bio::Assembly::ContigAnalysis( -contig=>$contigOBJ ); my @lcq = $ca->low_consensus_quality; my @hqd = $ca->high_quality_discrepancies; my @ss = $ca->single_strand_regions; 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.

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: rfsouza@citri.iq.usp.br The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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

_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