Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature =head1 LICENSE Copyright (c) 1999-2009 The European Bioinformatics Institute and Genome Research Limited. All rights reserved. This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at <ensembl-dev@ebi.ac.uk>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. =head1 AUTHOR Juguang Xiao <juguang@tll.org.sg> =cut =head1 NAME Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature =head1 SYNOPISIS Please read Bio::EnsEMBL::Utils::Converter =head1 DESCRIPTION =head1 METHODS =cut package Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature; use strict; use vars qw(@ISA); use Bio::EnsEMBL::SeqFeature; use Bio::EnsEMBL::SimpleFeature; use Bio::EnsEMBL::Exon; use Bio::EnsEMBL::Utils::Converter::bio_ens; @ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens); sub _convert_single { my ($self, $in) = @_; unless($in && defined($in) && $in->isa('Bio::SeqFeature::Generic')){ $self->throw("a Bio::SeqFeature::Generic object needed"); } my $seqFeature = $in; my $seq_id = $seqFeature->seq_id; unless(defined($seq_id) && $seq_id){ $self->warn("No seq_id value. EnsEMBL SeqFeature will validate it"); $seq_id = 'Unknown'; } # Debated issue here. There are p_value and percent_id in EnsEMBL API and DB # schema, but not in bioperl. If in bioperl there are tags called p_value or # percent_id, then the values are passed, otherwise set the default 1. # # the problem arise when I try to converter the seqfeature for tmhmm to # EnsEMBL seqFeature. # -- Juguang, 11 July '03 my $score = $in->score || 0; my $percent_id; if($in->has_tag('percent_id')){ ($percent_id) = $in->get_tag_values('percent_id'); }else{ $percent_id ||= 0; } my $p_value; if($in->has_tag('p_value')){ ($p_value) = $in->get_tag_values('p_value'); }elsif($in->has_tag('evalue')){ ($p_value) = $in->get_tag_values('evalue'); }else{ $p_value ||= 1; } my $ens_seqFeature; my %args = ( -start => $in->start, -end => $in->end, -strand => $in->strand, -score => $score, -analysis => $self->analysis, -source_tag => $in->source_tag, -seqname => $seq_id, -percent_id => $percent_id, -p_value => $p_value ); my $output_module = $self->out; if($output_module eq 'Bio::EnsEMBL::SeqFeature'){ $ens_seqFeature = new Bio::EnsEMBL::SeqFeature(%args); }elsif($self->out eq 'Bio::EnsEMBL::SimpleFeature'){ $ens_seqFeature = new Bio::EnsEMBL::SimpleFeature(%args); # The field that there is in SimpleFeature, but not in SeqFeature. $ens_seqFeature->display_label('__NONE__'); }elsif($self->out eq 'Bio::EnsEMBL::Exon'){ $ens_seqFeature = Bio::EnsEMBL::Exon->new_fast( $self->contig, $seqFeature->start, $seqFeature->end, $seqFeature->strand); }elsif($self->out eq 'Bio::EnsEMBL::ProteinFeature'){ my $seq_id2 = $self->analysis->logic_name; unless(defined $self->translation_id){ $self->throw('translation_id unset, in ProteinFeature conversion'); } $args{'-seqname'} = $self->translation_id; $ens_seqFeature = Bio::EnsEMBL::ProteinFeature->new( -feature1 => Bio::EnsEMBL::SeqFeature->new(%args), -feature2 => Bio::EnsEMBL::SeqFeature->new( -start => 0, -end => 0, -seqname => $seq_id2 ) ); }else{ $self->throw("[$output_module] as -out, not supported"); } $ens_seqFeature->attach_seq($self->contig); return $ens_seqFeature; } 1;