# $Id: Utils.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Coordinate::Utils # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects =head1 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); =head1 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 L, L, and L for more. =head1 FEEDBACK =head2 Mailing Lists 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: http://bugzilla.open-bio.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org Jason Stajich jason at bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Coordinate::Utils; use Bio::Location::Simple; use Bio::Coordinate::Pair; use Bio::Coordinate::Collection; use strict; use base qw(Bio::Root::Root); # new inherited from Root =head2 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 =cut 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; } =head2 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 =cut 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;