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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Assembly::ContigAnalysis \- Perform analysis on sequence assembly contigs. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& # 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; .Ve .SH "DESCRIPTION" .IX Header "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. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Robson Francisco de Souza" .IX Header "AUTHOR - Robson Francisco de Souza" Email: rfsouza@citri.iq.usp.br .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SH "Object creator" .IX Header "Object creator" .SS "new" .IX Subsection "new" .Vb 6 \& 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 .Ve .SH "Analysis methods" .IX Header "Analysis methods" .SS "high_quality_discrepancies" .IX Subsection "high_quality_discrepancies" .Vb 3 \& 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 .Ve .SS "low_consensus_quality" .IX Subsection "low_consensus_quality" .Vb 10 \& 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 .Ve .SS "not_confirmed_on_both_strands" .IX Subsection "not_confirmed_on_both_strands" .Vb 3 \& 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 .Ve .SS "single_strand" .IX Subsection "single_strand" .Vb 3 \& 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\*(Aqs 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 .Ve .SH "Internal Methods" .IX Header "Internal Methods" .SS "_merge_overlapping_features" .IX Subsection "_merge_overlapping_features" .Vb 6 \& 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 .Ve .SS "_complementary_features_list" .IX Subsection "_complementary_features_list" .Vb 9 \& 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 .Ve