=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut =head1 NAME Bio::EnsEMBL::ProteinFeature =head1 SYNOPSIS my $feature = Bio::EnsEMBL::ProteinFeature->new( -start => $start, -end => $end, -hstart => $hit_start, -hend => $hit_end, -hseqname => $hit_name ); =head1 DESCRIPTION ProteinFeature objects represent domains or other features of interest on a peptide sequence. =head1 METHODS =cut package Bio::EnsEMBL::ProteinFeature; use strict; use Bio::EnsEMBL::FeaturePair; use Bio::EnsEMBL::BaseAlignFeature; use Bio::EnsEMBL::Utils::Argument qw(rearrange); use parent qw(Bio::EnsEMBL::BaseAlignFeature); =head2 new Arg [IDESC] : (optional) string An interpro description Arg [INTERPRO_AC] : (optional) string An interpro accession Arg [TRANSLATION_ID] : (optional) integer A translation dbID Arg [...] : named arguments to FeaturePair superclass Example : $pf = Bio::EnsEMBL::ProteinFeature->new( -IDESC => $idesc, -INTERPRO_AC => $iac, @fp_args ); Description: Instantiates a Bio::EnsEMBL::ProteinFeature Returntype : Bio::EnsEMBL::FeaturePair Exceptions : none Caller : general Status : Stable =cut sub new { my ($proto, @args) = @_; my $class = ref($proto) || $proto; my $self; my ($idesc, $ilabel, $interpro_ac, $translation_id, $external_data, $hit_description, $cigar_string, $align_type, $slice) = rearrange(['IDESC', 'ILABEL', 'INTERPRO_AC', 'TRANSLATION_ID', 'EXTERNAL_DATA', 'HDESCRIPTION', 'CIGAR_STRING', 'ALIGN_TYPE', 'SLICE'], @args); # BaseAlignFeature expects cigar_line or features if($cigar_string && $align_type){ $self = $class->SUPER::new(@args); }else{ #call the grand parent directly $self = $class->Bio::EnsEMBL::FeaturePair::new(@args); } # the strand of protein features is always 0 $self->{'strand'} = 0; $self->{'idesc'} = $idesc || ''; $self->{'ilabel'} = $ilabel || ''; $self->{'interpro_ac'} = $interpro_ac || ''; $self->{'translation_id'} = $translation_id || ''; $self->{'external_data'} = $external_data || ''; $self->{'hit_description'} = $hit_description || ''; $self->{'cigar_string'} = $cigar_string || ''; $self->{'align_type'} = $align_type; return $self; } =head2 strand Arg [1] : Ignored Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow : the strand to be set. Returntype : int Status : Stable =cut #do not allow the strand to be set sub strand { my $self = shift; return $self->{'strand'}; } =head2 idesc Arg [1] : (optional) string The interpro description Example : print $protein_feature->idesc(); Description: Getter/Setter for the interpro description of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub idesc { my $self = shift; $self->{'idesc'} = shift if (@_); return $self->{'idesc'}; } =head2 ilabel Arg [1] : (optional) string The interpro label Example : print $protein_feature->ilabel(); Description: Getter/Setter for the interpro label of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub ilabel { my $self = shift; $self->{'ilabel'} = shift if (@_); return $self->{'ilabel'}; } =head2 interpro_ac Arg [1] : (optional) string The interpro accession Example : print $protein_feature->interpro_ac(); Description: Getter/Setter for the interpro accession of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub interpro_ac { my $self = shift; $self->{'interpro_ac'} = shift if (@_); return $self->{'interpro_ac'}; } =head2 translation_id Arg [1] : (optional) integer The dbID of the translation Example : print $protein_feature->translation_id(); Description: Getter/Setter for the translation dbID of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub translation_id { my $self = shift; $self->{'translation_id'} = shift if (@_); return $self->{'translation_id'}; } sub external_data { my $self = shift; $self->{'external_data'} = shift if (@_); return $self->{'external_data'}; } =head2 summary_as_hash Example : $protein_feature_summary = $protein_feature->summary_as_hash(); Description : Retrieves a textual summary of this Protein feature. Not inherited from Feature. Returns : hashref of arrays of descriptive strings Status : Intended for internal use =cut sub summary_as_hash { my $self = shift; my %summary; $summary{'type'} = $self->analysis->db; $summary{'id'} = $self->display_id; $summary{'start'} = $self->start; $summary{'end'} = $self->end; $summary{'interpro'} = $self->interpro_ac; $summary{'description'} = $self->idesc; $summary{'hit_start'} = $self->hstart; $summary{'hit_end'} = $self->hend; $summary{'cigar_string'} = $self->cigar_string; $summary{'align_type'} = $self->align_type; $summary{'hseqname'} = $self->hseqname; $summary{'translation_id'} = $self->translation_id; return \%summary; } =head2 alignment_strings Arg [1] : list of string $flags Example : $pf->alignment_strings Description: Allows to rebuild the alignment string of both the query and target sequence using the sequence from translation object and MD Z String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* (Refer: SAM/BAM specification) eg: MD:Z:96^RHKTDSFVGLMGKRALNS0V14 Returntype : array reference containing 2 strings the first corresponds to seq the second corresponds to hseq Exceptions : none Caller : general Status : Stable =cut sub alignment_strings { my $self = shift; #Translations my $transl_adaptor = $self->adaptor->db->get_TranslationAdaptor(); my $transl_object = $transl_adaptor->fetch_by_dbID($self->translation_id); my $seq; if(defined $transl_object && $transl_object->isa('Bio::EnsEMBL::Translation')) { $seq = $transl_object->transcript()->translate()->seq(); } if ($self->align_type eq 'mdtag') { if(defined $seq && defined $self->cigar_string){ return $self->_mdz_alignment_string($seq,$self->cigar_string); }else{ warn "sequence or cigar_line not found for " . $self->translation_id; } } else { throw("alignment_strings method not implemented for " . $self->align_type); } return; } sub transform { my $self = shift; $self->throw( "ProteinFeature cant be transformed directly as". " they are not on EnsEMBL coord system" ); return; } =head2 _hit_unit Arg [1] : none Description: PRIVATE implementation of abstract superclass method. Returns 1 as the 'unit' used for the hit sequence. Returntype : int Exceptions : none Caller : Bio::EnsEMBL::BaseAlignFeature Status : Stable =cut sub _hit_unit { return 3; } =head2 _query_unit Arg [1] : none Description: PRIVATE implementation of abstract superclass method. Returns 3 as the 'unit' used for the query sequence. Returntype : int Exceptions : none Caller : Bio::EnsEMBL::BaseAlignFeature Status : Stable =cut sub _query_unit { return 3; } 1;