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