Raw content of SupportingEvidenceInfo
<![CDATA[package SupportingEvidenceInfo;
=pod
=head1 NAME
SupportingEvidenceInfo
=head1 SYNOPSIS
A module to identify supporting evidence associated with transcripts and
genes on the basis of both gene ids and evidence ids
=head1 DESCRIPTION
This module can be given an evidence id (either protein or cdna) or a gene
or transcript id then find either the gene ids which it supports of the
evidence which supports it
=head1 CONTACT
ensembl dev mailing list <ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
use vars qw(@ISA $AUTOLOAD);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw( );
sub new{
my ($class, @args) = @_;
my $self = bless {},$class;
return $self;
}
=head2 Container methods
Arg [1] : SupportingEvidenceInfo
Arg [2] : value of variable
Function : container for specified variable. This pod refers to the
seven methods below, db, verbose, info, evidence_type, id_type
have_pfetch and primary_evidence. These are simple containers which do no
more than hold and return an given value
Returntype: value of variable
Exceptions: some throw if type is incorrect
Example : my $db = SupportingEvidenceInfo->db;
=cut
sub db{
my ($self, $db) = @_;
if($db){
if(!($db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))){
throw("Must pass SupportingEvidenceInfo:db a DBAdaptor not a $db");
}
$self->{'db'} = $db;
}
return $self->{'db'};
}
sub verbose{
my ($self, $value) = @_;
if(defined($value)){
$self->{'verbose'} = $value;
}
return $self->{'verbose'};
}
sub info{
my ($self, $value) = @_;
if(defined($value)){
$self->{'info'} = $value;
}
return $self->{'info'};
}
sub evidence_type{
my ($self, $value) = @_;
if($value){
$self->{'evidence_type'} = $value;
}
return $self->{'evidence_type'} || 'protein_align_feature';
}
sub id_type{
my ($self, $value) = @_;
if($value){
$self->{'id_type'} = $value;
}
return $self->{'id_type'} || 'gene';
}
sub have_pfetch{
my ($self, $value) = @_;
if(defined($value)){
$self->{'have_pfetch'} = $value;
}
return $self->{'have_pfetch'};
}
sub primary_evidence{
my ($self, $value) = @_;
if(defined($value)){
$self->{'primary_evidence'} = $value;
}
return $self->{'primary_evidence'};
}
=head2 evidence_ids_from_feature_id
Arg [1] : SupportingEvidenceInfo
Arg [2] : int, transcript or gene dbID
Arg [3] : string, table name, gene or transcript
Arg [4] : string, evidence type dna_align_feature or protein_align_feature
Arg [5] : Bio::EnsEMBL::DBSQL::DBAdaptor
Function : find which evidence ids of the type specified are associated
with this dbID
Returntype: none
Exceptions: none
Example : $supportingevidenceinfo->(1);
=cut
sub evidence_ids_from_feature_id{
my ($self, $transcript_id, $id_type, $evidence_type, $primary, $db) = @_;
if(!$db){
$db = $self->db;
}
if(!$evidence_type){
$evidence_type = $self->evidence_type;
}
if(!$id_type){
$id_type = $self->id_type;
}
if(!$primary){
$primary = $self->primary_evidence;
}
my @protein_ids;
my $sql;
if($primary){
$sql = $self->primary_evidence_from_feature_id_sql($transcript_id,
$evidence_type,
$id_type);
}else{
$sql = $self->evidence_from_feature_id_sql($transcript_id,
$evidence_type,
$id_type);
}
print "SQL: ".$sql."\n" if($self->verbose);
my $sth = $db->dbc->prepare($sql);
$sth->execute();
while(my ($protein_id) = $sth->fetchrow){
print"Have protein id ".$protein_id."\n" if($self->verbose);
push(@protein_ids, $protein_id);
}
$self->fetch_descriptions(\@protein_ids);
}
=head2 feature_ids_from_evidence_id
Arg [1] : SupportingEvidenceInfo
Arg [2] : string, evidence identifier
Arg [3] : string, gene type
Arg [4] : string, table name, gene or transcript
Arg [5] : string, evidence type dna_align_feature or
protein_align_feature
Arg [6] : Bio::EnsEMBL::DBSQL::DBAdaptor
Function : get the dbIDs of any genes or transcripts which have this
as part of their supporting evidence
Returntype: none
Exceptions: none
Example : $supportingevidenceinfo->
feature_ids_from_evidence_id('Q8K1F0');
=cut
sub feature_ids_from_evidence_id{
my ($self, $evidence_id, $gene_type, $evidence_type, $id_type,
$primary, $db) = @_;
if(!$db){
$db = $self->db;
}
if(!$evidence_type){
$evidence_type = $self->evidence_type;
}
if(!$id_type){
$id_type = $self->id_type;
}
if(!$primary){
$primary = $self->primary_evidence;
}
my $sql;
if($primary){
$sql = $self->feature_id_from_primary_evidence_sql($evidence_id,
$evidence_type,
$id_type,
$gene_type);
}else{
$sql = $self->feature_id_from_evidence_sql($evidence_id,
$evidence_type,
$id_type,
$gene_type);
}
print "SQL:".$sql."\n" if($self->verbose);
my $sth = $db->dbc->prepare($sql);
$sth->execute();
while(my ($feature_id) = $sth->fetchrow){
if($self->info){
print $evidence_id." ";
my $adaptor = $self->get_adaptor($id_type, $db);
my $feature = $adaptor->fetch_by_dbID($feature_id);
$self->print_feature_info($feature);
}else{
print $evidence_id ." ".$feature_id."\n";
}
}
}
sub dbID_from_stable_id{
my ($self, $stable_id, $id_type, $db) = @_;
$db = $self->db if(!$db);
$id_type = $self->id_type if(!$id_type);
my $sql = "select ".$id_type."_id ".
"from ".$id_type."_stable_id ".
"where stable_id = ?";
print "SQL: $sql \n" if($self->verbose);
my $sth = $db->dbc->prepare($sql);
$sth->execute($stable_id);
my ($dbID) = $sth->fetchrow;
return $dbID;
}
=head2 fetch_descriptions
Arg [1] : SupportingEvidenceInfo
Arg [2] : Arrayref (array of ids for pfetch)
Function : fetch descriptions for given identifiers from pfetch
Returntype: none
Exceptions: throws if faileds to open or close the pmatch command
Example : $self->fetch_descriptions(\@protein_ids);
=cut
sub fetch_descriptions{
my ($self, $protein_ids) = @_;
ID:foreach my $id(@$protein_ids){
if($id =~ /(S+)-\1/){
$id = 1;
}
if($self->have_pfetch){
my $command = "pfetch -D ".$id."\n";
print $command."\n" if($self->verbose);
open(FH, $command." | ") or throw("failed to open ".$command);
LINE:while(<FH>){
if(/no\s+match/){
print $id." has no match\n";
next LINE;
}
print;
}
close(FH) or throw("Failed to close $command");
}else{
print $id."\n";
}
}
}
=head2 print_feature_info
Arg [1] : SupportingEvidenceInfo
Arg [2] : Bio::EnsEMBL::Feature
Function : prints location information about feature give
Returntype: none
Exceptions: none
Example : $self->print_feature_info($transcript);
=cut
sub print_feature_info{
my ($self, $feature) = @_;
throw("Must pass print_feature_info a feature") if(!$feature);
my $info_string = $feature->dbID." ";
$info_string .= $feature->stable_id if($feature->stable_id);
$info_string .= $feature->slice->seq_region_name." ".
$feature->slice->coord_system_name." ".$feature->start." ".
$feature->end." ".$feature->strand."\n";
print $info_string."\n";
}
=head2 get_adaptor
Arg [1] : SupportingEvidenceInfo
Arg [2] : string, id type gene or transcript
Arg [3] : Bio::EnsEMBL::DBSQL::DBAdaptor
Function : get an appropriate buisness adaptor for the features
wanted
Returntype: Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
Exceptions: throws if not passed a recognised type
Example :
=cut
sub get_adaptor{
my ($self, $id_type, $db) = @_;
$db = $self->db if(!$db);
$id_type = $id_type if(!$id_type);
if($id_type eq 'gene'){
return $db->get_GeneAdaptor;
}elsif($id_type eq 'transcript'){
return $db->get_TranscriptAdaptor;
}
throw("Failed to get adaptor for feature type ".$id_type);
}
=head2 read_id_file
Arg [1] : SupportingEvidenceInfo
Arg [2] : string, filename
Function : read file to produce a list of ids, takes the first word
from each line
Returntype: arrayref
Exceptions: throws if fails to open or close file
Example : my $ids = SupportingEvidenceInfo->read_id_file($file)
=cut
sub read_id_file{
my ($self, $file) = @_;
open(FH, $file) or throw("Failed to open ".$file);
my @ids;
while(<FH>){
chomp;
my ($id) = split;
push(@ids, $id);
}
close(FH) or throw("Failed to close ".$file);
return \@ids;
}
#Methods to return the SQL
=head2 sql methods
Arg [1] : SupportingEvidenceInfo
Function : These methods all take arguments to be used to produce
an sql string to be used in order to fetch either evidence or feature
ids. What is different is if they fetch on the basis of primary evidence
associated with whole transcripts or all the evidence associated with each
exon
Returntype: string
Exceptions: none
Example :
=cut
sub primary_evidence_from_feature_id_sql{
my ($self, $feature_id, $evidence_type, $id_type) = @_;
my $sql = ("SELECT distinct(hit_name) ".
"FROM transcript, ".
"transcript_supporting_feature, ".
"$evidence_type ".
"WHERE transcript.".$id_type."_id = ".$feature_id." ".
"and transcript.transcript_id = ".
"transcript_supporting_feature.transcript_id ".
"and feature_type = '".$evidence_type."' ".
"and feature_id = ".$evidence_type."_id ");
return $sql;
}
sub evidence_from_feature_id_sql{
my ($self, $feature_id, $evidence_type, $id_type) = @_;
my $sql = ("select distinct(hit_name) ".
"from $evidence_type, supporting_feature, ".
"exon_transcript, exon, transcript ".
"where ".$evidence_type."_id = feature_id ".
"and feature_type = '$evidence_type'".
"and supporting_feature.exon_id = exon_transcript.exon_id ".
"and exon_transcript.transcript_id = ".
"transcript.transcript_id ".
"and transcript.".$id_type."_id = $feature_id");
return $sql;
}
sub feature_id_from_primary_evidence_sql{
my ($self, $evidence_id, $evidence_type, $id_type, $gene_type) = @_;
my $sql = ("SELECT distinct(transcript.".$id_type."_id) ".
"FROM transcript, transcript_supporting_feature, ".
"gene, $evidence_type ".
"WHERE transcript.gene_id = gene.gene_id ".
"and transcript.transcript_id = ".
"transcript_supporting_feature.transcript_id ".
"and feature_type = '$evidence_type' ".
"and feature_id = ".$evidence_type."_id ".
"and hit_name = '$evidence_id' ");
$sql .= "and biotype = '".$gene_type."' " if($gene_type);
return $sql;
}
sub feature_id_from_evidence_sql{
my ($self, $evidence_id, $evidence_type, $id_type, $gene_type) = @_;
my $sql = ("SELECT distinct(transcript.".$id_type."_id) ".
"FROM transcript, exon_transcript, supporting_feature, ".
"$evidence_type, gene ".
"WHERE hit_name = '$evidence_id' ".
"AND ".$evidence_type."_id = feature_id ".
"AND feature_type = '$evidence_type' ".
"AND supporting_feature.exon_id = exon_transcript.exon_id ".
"AND exon_transcript.transcript_id = ".
"transcript.transcript_id ".
"AND transcript.gene_id = gene.gene_id");
$sql .= " AND biotype = '".$gene_type."'" if($gene_type);
return $sql;
}
1;
]]>