Raw content of Bio::EnsEMBL::Analysis::Tools::FeatureFactory
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::Tools::FeatureFactory
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::Tools::FeatureFactory
=head1 SYNOPSIS
my $featurefactory = new Bio::EnsEMBL::Analysis::Tools::FeatureFactory;
my $feature_pair = $featurefactory->create_feature_pair(1, 13, -1, 300,
45, 56, 1 Q12732,
95, 2.3e-35, '',
$slice,
$analysis);
$featurefactory->validate($feature_pair);
=head1 DESCRIPTION
This is a utilities module which provides methods for feature creation
and feature validation for various feature types
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::Tools::FeatureFactory;
use strict;
use warnings;
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::RepeatFeature;
use Bio::EnsEMBL::RepeatConsensus;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::DnaPepAlignFeature;
use Bio::EnsEMBL::MiscFeature;
use Bio::EnsEMBL::Attribute;
use Bio::EnsEMBL::MiscSet;
use Bio::EnsEMBL::PredictionTranscript;
use Bio::EnsEMBL::PredictionExon;
use Bio::EnsEMBL::SimpleFeature;
use Bio::EnsEMBL::Map::Marker;
use Bio::EnsEMBL::Map::MarkerFeature;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Analysis::Programs;
use vars qw (@ISA);
@ISA = qw();
sub new{
my ($class,@args) = @_;
my $self = bless {},$class;
return $self;
}
#feature creation methods#
=head2 create_simple_feature
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : int, start
Arg [3] : int, end,
Arg [4] : int, stand (must be 0, 1 or -1)
Arg [5] : int score,
Arg [6] : string, display label,
Arg [7] : string, sequence name
Arg [8] : Bio::EnsEMBL::Slice
Arg [9] : Bio::EnsEMBL::Analysis
Function : creata a Bio::EnsEMBL::SimpleFeature
Returntype: Bio::EnsEMBL::SimpleFeature
Exceptions:
Example :
=cut
sub create_simple_feature{
my ($self, $start, $end, $strand, $score, $display_label,
$seqname, $slice, $analysis) = @_;
my $simple_feature = Bio::EnsEMBL::SimpleFeature->new
(
-start => $start,
-end => $end,
-strand => $strand,
-score => $score,
-display_label => $display_label,
-seqname => $seqname,
-slice => $slice,
-analysis => $analysis,
);
return $simple_feature;
}
=head2 create_simple_feature
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : string, name
Arg [3] : string, class
Arg [4] : string, type
Arg [5] : string, consensus sequence
Arg [6] : int length
Function : creata a Bio::EnsEMBL::RepeatConsensus
Returntype: Bio::EnsEMBL::RepeatConsensus
Exceptions:
Example :
=cut
sub create_repeat_consensus{
my ($self, $name, $class, $type, $consensus_seq, $length) = @_;
my $repeat_consensus = Bio::EnsEMBL::RepeatConsensus->new
(
-name => $name,
-length => $length,
-repeat_class => $class,
-repeat_consensus => $consensus_seq,
-repeat_type => $type,
);
return $repeat_consensus;
}
=head2 create_simple_feature
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : int, start
Arg [3] : int, end,
Arg [4] : int, stand (must be 0, 1 or -1)
Arg [5] : int score,
Arg [6] : int, repeat_start
Arg [7] : int, repeat_end
Arg [8] : Bio::EnsEMBL::RepeatConsensus
Arg [9] : Bio::EnsEMBL::Slice
Arg [10] : Bio::EnsEMBL::Analysis
Function : creata a Bio::EnsEMBL::RepeatFeature
Returntype: Bio::EnsEMBL::RepeatFeature
Exceptions:
Example :
=cut
sub create_repeat_feature{
my ($self, $start, $end, $strand, $score, $repeat_start, $repeat_end,
$repeat_consensus, $seqname, $slice, $analysis) = @_;
my $repeat_feature = Bio::EnsEMBL::RepeatFeature->new
(
-start => $start,
-end => $end,
-strand => $strand,
-slice => $slice,
-analysis => $analysis,
-repeat_consensus => $repeat_consensus,
-hstart => $repeat_start,
-hend => $repeat_end,
-score => $score,
-seqname => $seqname,
);
return $repeat_feature;
}
=head2 create_feature_pair
Arg [1] : Bio::EnsEMBL::Analysis::Runnable
Arg [2] : int, start
Arg [3] : int, end
Arg [4] : int, strand must be 0, 1 or -1
Arg [5] : int, score
Arg [6] : int, hstart
Arg [7] : int, hend
Arg [8] : int, hstrand
Arg [9] : string, hseqname
Arg [10] : int, percent id
Arg [11] : int, p value
Arg [12] : string, seqname
Arg [13] : Bio::EnsEMBL::Slice
Arg [14] : Bio::EnsEMBL::Analysis
Function : creates a Bio::EnsEMBL::FeaturePair
Returntype: Bio::EnsEMBL::FeaturePair
Exceptions:
Example :
=cut
sub create_feature_pair {
my ($self, $start, $end, $strand, $score, $hstart, $hend,
$hstrand, $hseqname, $percent_id, $p_value, $seqname,
$slice, $analysis, $positive_matches, $identical_matches) = @_;
my $fp = Bio::EnsEMBL::FeaturePair->new(
-start => $start,
-end => $end,
-strand => $strand,
-hstart => $hstart,
-hend => $hend,
-hstrand => $hstrand,
-percent_id => $percent_id,
-score => $score,
-p_value => $p_value,
-hseqname => $hseqname,
-analysis => $analysis,
);
$fp->seqname($seqname);
$fp->slice($slice);
$fp->positive_matches($positive_matches);
$fp->identical_matches($identical_matches);
return $fp;
}
=head2 create_misc_feature
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : int, start,
Arg [3] : int, end
Arg [4] : int, strand
Arg [5] : Bio::EnsEMBL::Slice
=cut
sub create_misc_feature {
my ($self, $start, $end, $strand, $slice) = @_;
my $mf = Bio::EnsEMBL::MiscFeature->new
(
-start => $start,
-end => $end,
-strand => $strand,
-slice => $slice,
);
return $mf;
}
=head2 add_misc_feature_attribute
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : Bio::EnsEMBL::MiscFeature
Arg [3] : string, code
Arg [4] : string, name
Arg [5] : string, description
Arg [6] : string, value
=cut
sub add_misc_feature_attribute {
my ($self, $mf, $code, $name, $description, $value) = @_;
$mf->add_Attribute ( Bio::EnsEMBL::Attribute->new
(-CODE => $code,
-NAME => $name,
-DESCRIPTION => $description,
-VALUE => $value,
)
);
}
=head2 add_misc_set
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : Bio::EnsEMBL::MiscFeature
Arg [3] : string, code
Arg [4] : string, name
Arg [5] : string, description
Arg [6] : string, value
=cut
sub add_misc_set {
my ($self, $mf, $code, $name, $description, $longest_feature) = @_;
$mf->add_MiscSet ( Bio::EnsEMBL::MiscSet->new
(-CODE => $code,
-NAME => $name,
-DESCRIPTION => $description,
-VALUE => $longest_feature,
)
);
}
=head2 create_prediction_exons
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : int, start,
Arg [3] : int, end
Arg [4] : int, strand
Arg [5] : int, score
Arg [6] : float, p value
Arg [7] : int, phase
Arg [8] : string, seqname
Arg [9] : Bio::EnsEMBL::Slice
Arg [10] : Bio::EnsEMBL::Analysis
Function : create a Bio::EnsEMBL::PredictionExon
Returntype: Bio::EnsEMBL::PredictionExon
Exceptions:
Example :
=cut
sub create_prediction_exon{
my ($self, $start, $end, $strand, $score, $pvalue, $phase, $seqname,
$slice, $analysis) = @_;
my $exon = Bio::EnsEMBL::PredictionExon->new
(
-start => $start,
-end => $end,
-strand => $strand,
-score => $score,
-p_value => $pvalue,
-phase => $phase,
-slice => $slice,
-seqname => $seqname,
-analysis => $analysis,
);
return $exon;
}
=head2 create_prediction_transcript
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : arrayref, array of Bio::EnsEMBL::PredictionExons
Arg [3] : Bio::EnsEMBL::Slice
Arg [4] : Bio::EnsEMBL::Analysis
Function :
Returntype:
Exceptions:
Example :
=cut
sub create_prediction_transcript{
my ($self, $exons, $slice, $analysis) = @_;
my $transcript = Bio::EnsEMBL::PredictionTranscript->new
(
-exons => $exons,
-slice => $slice,
-analysis => $analysis,
);
return $transcript;
}
=head2 create_marker
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : int, database id
Function : create a marker with a specific database id
Returntype: Bio::EnsEMBL::Map::Marker
Exceptions:
Example :
=cut
sub create_marker{
my ($self, $dbID) = @_;
my $m = Bio::EnsEMBL::Map::Marker->new();
$m->dbID($dbID);
return $m;
}
=head2 create_marker_feature
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : int, start
Arg [3] : int, end
Arg [4] : int, strand
Arg [5] : Bio::EnsEMBL::Map::Marker
Arg [6] : string, seqname
Arg [7] : Bio::EnsEMBL::Slice
Arg [8] : Bio::EnsEMBL::Analysis
Function :
Returntype: Bio::EnsEMBL::Map::MarkerFeature
Exceptions:
Example :
=cut
sub create_marker_feature{
my ($self, $start, $end, $strand, $marker,
$seqname, $slice, $analysis) = @_;
my $mf = Bio::EnsEMBL::Map::MarkerFeature->new();
$mf->start($start);
$mf->end($end);
$mf->strand($strand);
$mf->marker($marker);
$mf->seqname($seqname);
$mf->slice($slice);
$mf->analysis($analysis);
return $mf;
}
#validation methods#
=head2 validate
Arg [1] : Bio::EnsEMBL::Analysis::Tools::FeatureFactory
Arg [2] : Bio::EnsEMBL::Feature
Function : validates feature
Returntype: Bio::EnsEMBL::Feature
Exceptions: throws if no slice or analysis is defined
if the start, end or strand arent defined, if start or end are
less than one or if start is greater than end
Example :
=cut
sub validate{
my ($self, $feature) = @_;
# print STDERR "validating: ".$feature->start."-".$feature->end.":".$feature->hseqname."::".$feature->hstart."-".$feature->hend."\n";
my @error_messages;
if(!$feature){
throw("Can't validate a feature without a feature ".
"FeatureFactory::validate");
}
if(!($feature->isa('Bio::EnsEMBL::Feature'))){
throw("Wrong type ".$feature." must be a Bio::EnsEMBL::Feature ".
"object FeatureFactory::validate");
}
if(not defined $feature->slice){
my $string = "No slice defined";
push(@error_messages, $string);
}
if(not defined $feature->analysis){
my $string = "No analysis defined";
push(@error_messages, $string);
}
if(not defined $feature->start){
my $string = "No start defined";
push(@error_messages, $string);
}
if(not defined $feature->end){
my $string = "No end defined";
push(@error_messages, $string);
}
if(not defined $feature->strand){
my $string = "No strand defined";
push(@error_messages, $string);
}
if($feature->start > $feature->end){
my $string = "Start is greater than end ".$feature->start." ".
$feature->end;
push(@error_messages, $string);
}
if(@error_messages > 0){
print STDERR join("\n", @error_messages);
throw("Invalid feature ".$feature." FeatureFactory:validate");
}
}
sub validate_prediction_transcript{
my ($self, $pt, $attach_to_exons) = @_;
if(!$pt){
throw("Can't validate a prediction transcript without a ".
"prediction transcript ".
"FeatureFactory:validate_prediction_transcript");
}
if(!($pt->isa('Bio::EnsEMBL::PredictionTranscript'))){
throw("Wrong type ".$pt." must be a Bio::EnsEMBL::PredictionTranscript".
"FeatureFactory:validate_prediction_transcript");
}
my @exons = @{$pt->get_all_Exons};
if(@exons == 0){
throw("problem ".$pt." has no exons");
}
foreach my $e(@exons){
if($attach_to_exons){
$e->slice($pt->slice) if(!$e->slice);
$e->analysis($pt->analysis) if(!$e->analysis);
}
$self->validate($e);
}
$self->validate($pt);
my $tseq;
eval{
$tseq = $pt->translate;
};
if(!$tseq){
throw($pt." translate didn't return a sequence $@");
}
if ($tseq->seq =~ /\*/) {
my $msg = $pt." doesn't have a valid translation ".$tseq->seq;
$msg .= "\n$@" if($@);
throw($msg);
}
return 1;
}
1;
]]>