Bio::Coordinate Utils
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Summary
Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects
Package variables
No package variables defined.
Included modules
Bio::Coordinate::Collection
Bio::Coordinate::Pair
Bio::Location::Simple
Inherit
Bio::Root::Root
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.
Methods
from_alignDescriptionCode
from_seq_to_alignmentposDescriptionCode
Methods description
from_aligncode    nextTop
 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_alignmentposcodeprevnextTop
 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
Methods code
from_aligndescriptionprevnextTop
sub from_align {
   my ($self, $aln, $ref ) = @_;

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

   # 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:
$aln->map_chars('\.','-'); my $cs = $aln->gap_line; my $seq1 = $aln->get_seq_by_pos(1); my $seq2 = $aln->get_seq_by_pos(2); while ( $cs =~ /([^\-]+)/g) { # alignment coordinates
my $lenmatch = length($1); my $start = pos($cs) - $lenmatch +1; my $end = $start + $lenmatch -1; 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 ); unless( $pair->test ) { $self->warn(join("", "pair align did not pass test ($start..$end):\n", "\tm1=",$match1->to_FTstring(), " len=", $match1->length, " m2=", $match2->to_FTstring()," len=", $match2->length,"\n")); } $collection->add_mapper($pair); } return ($collection->each_mapper)[0] if $collection->mapper_count == 1; return $collection;
}
from_seq_to_alignmentposdescriptionprevnextTop
sub from_seq_to_alignmentpos {
    my ($self, $aln ) = @_;

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

    # default reference sequence to the first sequence
my @mappers; $aln->map_chars('\.','-'); for my $seq ( $aln->each_seq ) { my $collection = Bio::Coordinate::Collection->new(-return_match=>1); my $cs = $seq->seq(); # do we change this over to use index and substr for speed?
while ( $cs =~ /([^\-]+)/g) { # alignment coordinates
my $lenmatch = length($1); my $start = pos($cs) - $lenmatch +1; my $end = $start + $lenmatch -1; my $match1 = Bio::Location::Simple->new (-seq_id => $seq->id, -start => $seq->location_from_column($start)->start, -end => $seq->location_from_column($end)->start, -strand => $seq->strand ); my $match2 = Bio::Location::Simple->new (-seq_id => 'alignment', -start => $start, -end => $end, -strand => 0 ); my $pair = Bio::Coordinate::Pair->new (-in => $match1, -out => $match2 ); unless ( $pair->test ) { $self->warn(join("", "pair align did not pass test ($start..$end):\n", "\tm1=",$match1->to_FTstring(), " len=", $match1->length, " m2=", $match2->to_FTstring()," len=", $match2->length,"\n")); } $collection->add_mapper($pair); } if( $collection->mapper_count == 1) { push @mappers, ($collection->each_mapper)[0]; } else { push @mappers, $collection; } } return @mappers; } 1;
}
General documentation
FEEDBACKTop
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.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
Jason Stajich jason at bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _