Bio::Coordinate Utils
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Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects
Package variables
No package variables defined.
Included modules
    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);
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.
Methods description
from_aligncode    nextTop
 Title   : from_align
Usage : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
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
Methods code
sub from_align {
   my ($self, $aln, $ref ) = @_;

   $aln->isa('Bio::Align::AlignI') ||
       $self->throw('Not a Bio::Align::AlignI object but ['. ref($self). ']');

   # default reference sequence to the first sequence
$ref ||= 1; my $collection = Bio::Coordinate::Collection->new(-return_match=>1); # this works only for pairs, so split the MSA
# take the ref
#foreach remaining seq in aln, do:
my $cs = $aln->consensus_string(49); while ( $cs =~ /([^-]+)/g) { # alignment coordinates
my $start = pos($cs) - length($1) + 1; my $end = $start+length($1)-1; my $seq1 = $aln->get_seq_by_pos(1); my $seq2 = $aln->get_seq_by_pos(2); my $match1 = Bio::Location::Simple->new (-seq_id => $seq1->id, -start => $seq1->location_from_column($start)->start, -end => $seq1->location_from_column($end)->start, -strand => $seq1->strand ); my $match2 = Bio::Location::Simple->new (-seq_id => $seq2->id, -start => $seq2->location_from_column($start)->start, -end => $seq2->location_from_column($end)->start, -strand => $seq2->strand ); my $pair = Bio::Coordinate::Pair-> new(-in => $match1, -out => $match2 ); $collection->add_mapper($pair); } return @{$collection->each_mapper}[0] if $collection->each_mapper == 1; return $collection; } 1;
General documentation
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.                        - General discussion - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
AUTHOR - Heikki LehvaslaihoTop
     EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _