| Bio::Assembly::ContigAnalysis(3pm) | User Contributed Perl Documentation | Bio::Assembly::ContigAnalysis(3pm) |
Bio::Assembly::ContigAnalysis -
Perform analysis on sequence assembly contigs.
# 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;
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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
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
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
| 2018-10-27 | perl v5.26.2 |