Raw content of Bio::Tools::Promoterwise # BioPerl module for Bio::Tools::Promoterwise # # Cared for by Shawn Hoon <shawnh@fugu-sg.org> # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Promoterwise - DESCRIPTION of Object =head1 SYNOPSIS use Bio::Tools::Promoterwise; my $pw = Bio::Tools::Promoterwise->new(-file=>"out", -query1_seq=>$seq1, -query2_seq=>$seq2); while (my $fp = $pw->next_result){ print "Hit Length: ".$fp->feature1->length."\n"; print "Hit Start: ".$fp->feature1->start."\n"; print "Hit End: ".$fp->feature1->end."\n"; print "Hsps: \n"; my @first_hsp = $fp->feature1->sub_SeqFeature; my @second_hsp = $fp->feature2->sub_SeqFeature; foreach my $i (0..$#first_hsp){ print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ". $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n"; } } =head1 DESCRIPTION Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for promoter sequence alignments. Promoterwise is written by Ewan Birney. It is part of the wise2 package available at: ftp://ftp.ebi.ac.uk/pub/localsw/unix/wise2/ This module is the parser for the Promoterwise output in tab format. =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 the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =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::Tools::Promoterwise; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use Bio::Root::IO; @ISA = qw(Bio::Root::Root Bio::Root::IO ); =head2 new Title : new Usage : my $obj = new Bio::Tools::Promoterwise(); Function: Builds a new Bio::Tools::Promoterwise object Returns : L<Bio::Tools::Promoterwise> Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); my ($query1,$query2) = $self->_rearrange([qw(QUERY1_SEQ QUERY2_SEQ)],@args); $self->query1_seq($query1) if ($query1); $self->query2_seq($query2) if ($query2); return $self; } =head2 next_result Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : an L<Bio::SeqFeature::FeaturePair> Args : none =cut sub next_result { my ($self) = @_; $self->_parse unless $self->_parsed; return $self->_next_result; } sub _parse{ my ($self) = @_; my (%hash,@fp); while ($_=$self->_readline()) { chomp; my @array = split; push @{$hash{$array[$#array]}}, \@array; } foreach my $key(keys %hash){ my $sf1 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element", -source_tag=>"promoterwise"); $sf1->attach_seq($self->query1_seq) if $self->query1_seq; my $sf2 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element", -source_tag=>"promoterwise"); $sf2->attach_seq($self->query2_seq) if $self->query2_seq; foreach my $info(@{$hash{$key}}){ my ($score,$id1,$start_1,$end_1, $strand_1,$id2,$start_2,$end_2, $strand_2,$group)= @{$info}; if(!$sf1->strand && !$sf2->strand){ $sf1->strand($strand_1); $sf2->strand($strand_2); $sf1->seq_id($id1); $sf2->seq_id($id2); $sf1->score($score); $sf2->score($score); } my $sub1 = Bio::SeqFeature::Generic->new(-start=>$start_1, -seq_id=>$id1, -end =>$end_1, -strand=>$strand_1, -primary=>"conserved_element", -source_tag=>"promoterwise", -score=>$score); $sub1->attach_seq($self->query1_seq) if $self->query1_seq; my $sub2 = Bio::SeqFeature::Generic->new(-start=>$start_2, -seq_id=>$id2, -end =>$end_2, -strand=>$strand_2, -primary=>"conserved_element", -source_tag=>"promoterwise", -score=>$score); $sub2->attach_seq($self->query2_seq) if $self->query2_seq; $sf1->add_SeqFeature($sub1,'EXPAND'); $sf2->add_SeqFeature($sub2,'EXPAND'); } my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$sf1, -feature2=>$sf2); push @fp, $fp; } $self->_feature_pairs(\@fp); $self->_parsed(1); return; } sub _feature_pairs { my ($self,$fp) = @_; if($fp){ $self->{'_feature_pairs'} = $fp; } return $self->{'_feature_pairs'}; } sub _next_result { my ($self) = @_; return undef unless (exists($self->{'_feature_pairs'}) && @{$self->{'_feature_pairs'}}); return shift(@{$self->{'_feature_pairs'}}); } sub _parsed { my ($self,$flag) = @_; if($flag){ $self->{'_flag'} = 1; } return $self->{'_flag'}; } sub query1_seq { my ($self,$val) = @_; if($val){ $self->{'query1_seq'} = $val; } return $self->{'query1_seq'}; } sub query2_seq { my ($self,$val) = @_; if($val){ $self->{'query2_seq'} = $val; } return $self->{'query2_seq'}; } 1;