Bio::Assembly::ContigAnalysis(3pm) User Contributed Perl Documentation Bio::Assembly::ContigAnalysis(3pm)
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
perl v5.14.2 2012-03-02 Bio::Assembly::ContigAnalysis(3pm)