SYNOPSIS¶
use Bio::Coordinate::Utils;
# get a Bio::Align::AlignI compliant object, $aln, somehow
# it could be a Bio::SimpleAlign
$mapper = Bio::Coordinate::Utils->from_align($aln, 1);
# Build a set of mappers which will map, for each sequence,
# that sequence position in the alignment (exon position to alignment
# position)
my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);
DESCRIPTION¶
This class is a holder of methods that work on or create
Bio::Coordinate::MapperI- compliant objects. . These methods are not part of
the Bio::Coordinate::MapperI interface and should in general not be essential
to the primary function of sequence objects. If you are thinking of adding
essential functions, it might be better to create your own sequence class. See
Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more.
new¶
new() inherited from Root
from_align¶
Title : from_align
Usage : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
Function:
Create a mapper out of an alignment.
The mapper will return a value only when both ends of
the input range find a match.
Note: This implementation works only on pairwise alignments
and is not yet well tested!
Returns : A Bio::Coordinate::MapperI
Args : Bio::Align::AlignI object
Id for the reference sequence, optional
from_seq_to_alignmentpos¶
Title : from_seq_to_alignmentpos
Usage : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
Function:
Create a mapper out of an alignment.
The mapper will map the position of a sequence into that position
in the alignment.
Will work on alignments of >= 2 sequences
Returns : An array of Bio::Coordinate::MapperI
Args : Bio::Align::AlignI object