Bio::Assembly::ContigAnalysis.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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