Raw content of XrefMapper::drosophila_mojavensis
<![CDATA[package XrefMapper::drosophila_mojavensis;
use XrefMapper::BasicMapper;
use strict;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
use XrefMapper::BasicMapper qw(%stable_id_to_internal_id %object_xref_mappings %xref_to_source %xref_accessions %source_to_external_db);
my %genes_to_transcripts;
my %transcript_to_translation;
my %translation_to_transcript;
my %transcript_length;
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_mojavensis","*"]]];
}
sub gene_description_filter_regexps {
return ();
}
# Special logic for drosophila display_xrefs:
#
# gene: flybase_name if present, else gadfly_gene_cgid
#
# transcript: flybase_name if present, else gadfly_transcript_cgid
sub xref_offset{
my ($self, $val) = @_;
if(defined($val)){
$self->{'_xref_offset'} = $val;
}
return $self->{'_xref_offset'};
}
sub gene_display_xref_sources {
my @list = qw(
FlyBaseName_gene
FlyBaseCGID_gene
flybase_gene_id
);
my %ignore;
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
return [\@list,\%ignore];
}
sub build_transcript_and_gene_display_xrefs {
my ($self) = @_;
my $dir = $self->core->dir();
my %external_name_to_id;
my %ex_db_id_to_status;
my $sql1 = "SELECT external_db_id, db_name, status from external_db";
my $sth1 = $self->core->dbc->prepare($sql1) || die "prepare failed for $sql1\n";
$sth1->execute() || die "execute failed";
my ($db_id, $name, $status);
$sth1->bind_columns(\$db_id, \$name, \$status);
while($sth1->fetch()){
$external_name_to_id{$name} = $db_id;
$ex_db_id_to_status{$db_id} = $status;
}
$sth1->finish;
#############################
#create the tempory table
#############################
my $sth = $self->core->dbc->prepare("create table identity_xref_temp like identity_xref");
print "creating table identity_xref_temp\n";
$sth->execute() || die "Could not \ncreate table identity_xref_temp like identity_xref\n";
#############################
#populate the tempory table
#############################
my $file = $dir."/identity_xref_temp.txt";
if(-s $file){
my $sth = $self->core->dbc->prepare("LOAD DATA LOCAL INFILE \'$file\' IGNORE INTO TABLE identity_xref_temp");
print "Uploading data in $file to identity_xref_temp\n";
$sth->execute();
}
else{
print "NO file or zero size file, so not able to load file $file to identity_xref_temp\n";
}
#
# get a list of sources to use
# and also a list of those xrefs to ignore
# where the source name is the key and the value is the string to test for
#
my ($genepresedence, $geneignore) = @{$self->gene_display_xref_sources()};
my ($presedence, $ignore) = @{$self->transcript_display_xref_sources()};
my $i=0;
my %level;
foreach my $ord (reverse (@$presedence)){
$i++;
if(!defined($external_name_to_id{$ord})){
print STDERR "unknown external database name *$ord* being used\n";
}
$level{$external_name_to_id{$ord}} = $i;
}
foreach my $ord (reverse (@$genepresedence)){
$i++;
if(!defined($external_name_to_id{$ord})){
print STDERR "unknown external database name *$ord* being used\n";
}
$level{$external_name_to_id{$ord}} = $i;
}
if(!scalar(keys %genes_to_transcripts)){
$self->build_genes_to_transcripts();
}
if(!scalar(keys %translation_to_transcript)){
$self->load_translation_to_transcript();
}
my $sql = (<<ESQL);
SELECT ox.xref_id, ix.query_identity, ix.target_identity, x.external_db_id, x.display_label, e.db_name, ox.linkage_annotation
FROM (object_xref ox, xref x, external_db e)
LEFT JOIN identity_xref ix ON (ox.object_xref_id = ix.object_xref_id)
WHERE x.xref_id = ox.xref_id AND ox.ensembl_object_type = ?
AND ox.ensembl_id = ? AND x.info_type = 'SEQUENCE_MATCH'
AND e.external_db_id = x.external_db_id
ESQL
my $primary_sth = $self->core->dbc->prepare($sql) || die "prepare failed for $sql\n";
$sql = (<<ZSQL);
SELECT ox.xref_id, ix.query_identity, ix.target_identity, x.external_db_id, x.display_label, e.db_name, ox.linkage_annotation
FROM (object_xref ox, xref x, external_db e)
LEFT JOIN identity_xref_temp ix ON (ox.object_xref_id = ix.object_xref_id)
WHERE x.xref_id = ox.xref_id and ox.ensembl_object_type = ?
and ox.ensembl_id = ? and x.info_type = 'DEPENDENT'
AND e.external_db_id = x.external_db_id
ZSQL
my $dependent_sth = $self->core->dbc->prepare($sql) || die "prepare failed for $sql\n";
$sql = (<<QSQL);
SELECT x.xref_id, x.external_db_id, x.display_label, e.db_name, o.linkage_annotation
FROM object_xref o, xref x, external_db e
WHERE x.xref_id = o.xref_id
and o.ensembl_object_type = ? and o.ensembl_id = ? and x.info_type = 'DIRECT'
AND e.external_db_id = x.external_db_id
QSQL
my $direct_sth = $self->core->dbc->prepare($sql) || die "prepare failed for $sql\n";
# get xrefs connect directly to the gene.
$sql = (<<GSQL);
SELECT x.xref_id, x.external_db_id, e.db_name, o.linkage_annotation
FROM object_xref o, xref x, external_db e
WHERE x.xref_id = o.xref_id
and o.ensembl_object_type = 'Gene' and o.ensembl_id = ?
AND e.external_db_id = x.external_db_id
GSQL
my $gene_sth = $self->core->dbc->prepare($sql) || die "prepare failed for $sql\n";
my $count =0;
my ($xref_id, $qid, $tid, $ex_db_id, $display_label, $external_db_name, $linkage_annotation);
# Open file handles to recieve SQL and text data used to set
# display_xrefs
my $gene_dx_file = "$dir/gene_display_xref.sql";
my $tran_dx_file = "$dir/transcript_display_xref.sql";
my $unset_gene_dx_file = "$dir/gene_unset_display_xref.sql";
my $unset_tran_dx_file = "$dir/transcript_unset_display_xref.sql";
open (GENE_DX, ">$gene_dx_file")
or die( "Could not open $gene_dx_file: $!" );
open (TRANSCRIPT_DX, ">$tran_dx_file")
or die( "Could not open $tran_dx_file: $!" );
open (GENE_DX_UNSET, ">$unset_gene_dx_file")
or die( "Could not open $unset_gene_dx_file: $!" );
open (TRAN_DX_UNSET, ">$unset_tran_dx_file")
or die( "Could not open $unset_tran_dx_file: $!" );
open (GENE_DX_TXT, ">$dir/gene_display_xref.txt");
open (TRANSCRIPT_DX_TXT, ">$dir/transcript_display_xref.txt");
# These are the files that this method will return
my @files = ($unset_gene_dx_file,$gene_dx_file,
$unset_tran_dx_file,$tran_dx_file);
# Write the 'unset' sql to the files, and cose them
print GENE_DX_UNSET qq(UPDATE gene SET display_xref_id=NULL;\n);
print TRAN_DX_UNSET qq(UPDATE transcript SET display_xref_id=NULL;\n);
close( GENE_DX_UNSET );
close( TRAN_DX_UNSET );
# open (TRANSCRIPT_DX, ">$dir/transcript_display_xref.sql");
# open (TRANSCRIPT_DX_TXT, ">$dir/transcript_display_xref.txt");
# open (GENE_DX, ">$dir/gene_display_xref.sql");
# open (GENE_DX_TXT, ">$dir/gene_display_xref.txt");
#
foreach my $gene_id (keys %genes_to_transcripts) {
my %percent_id;
my %level_db;
my %parent;
my %percent_id_via_acc;
my @gene_xrefs = ();
$gene_sth->execute($gene_id) || die "execute failed";
$gene_sth->bind_columns(\$xref_id, \$ex_db_id, \$external_db_name, \$linkage_annotation);
my $best_gene_xref = 0; # store xref
my $best_gene_level = 0; # store level
my $best_gene_percent = 0; # additoon of precentage ids
while($gene_sth->fetch()){
if(defined($$ignore{$external_db_name})){
if($linkage_annotation =~ /$$ignore{$external_db_name}/){
# print "Ignoring $xref_id as linkage_annotation has ".$$ignore{$external_db_name}." in it. DELETE THIS MESSAGE AFTER TESTING\n";
next;
}
}
if($level{$ex_db_id} > $best_gene_level){
$best_gene_xref = $xref_id;
$best_gene_level = $level{$ex_db_id};
}
if($best_gene_xref){
print GENE_DX "UPDATE gene g SET g.display_xref_id=" . $best_gene_xref .
" WHERE g.gene_id=" . $gene_id . ";\n";
print GENE_DX_TXT $best_gene_xref . "\t" . $gene_id ."\n";
}
}
my @transcripts = @{$genes_to_transcripts{$gene_id}};
foreach my $transcript_id (@transcripts) {
my @transcript_xrefs = ();
foreach my $type ("Transcript", "Translation"){
my $ens_id;
if($type eq "Transcript"){
$ens_id = $transcript_id;
}
else{
if(defined($transcript_to_translation{$transcript_id})){
$ens_id=$transcript_to_translation{$transcript_id};
}
else{
next;
}
}
$primary_sth->execute($type, $ens_id ) || die "execute failed";
$primary_sth->bind_columns(\$xref_id, \$qid, \$tid, \$ex_db_id,
\$display_label, \$external_db_name,
\$linkage_annotation);
while($primary_sth->fetch()){
if($level{$ex_db_id} and $display_label =~ /\D+/ ){ #correct level and label is not just a number
if(defined($$ignore{$external_db_name})){
if($linkage_annotation =~ /$$ignore{$external_db_name}/){
# print "Ignoring $xref_id as linkage_annotation has ".$$ignore{$external_db_name}." in it. DELETE THIS MESSAGE AFTER TESTING\n";
next;
}
}
push @transcript_xrefs, $xref_id;
if(!defined($qid) || !defined($tid)){
print "PRIMARY $xref_id\n";
$percent_id{$xref_id} = 0;
}
else{
$percent_id{$xref_id} = $qid + $tid;
}
$level_db{$xref_id} = $level{$ex_db_id};
}
}
$dependent_sth->execute($type, $ens_id ) || die "execute failed";
$dependent_sth->bind_columns(\$xref_id, \$qid, \$tid, \$ex_db_id,
\$display_label, \$external_db_name,
\$linkage_annotation);
while($dependent_sth->fetch()){
if($level{$ex_db_id} and $display_label =~ /\D+/){
if(defined($$ignore{$external_db_name})){
if($linkage_annotation =~ /$$ignore{$external_db_name}/){
# print "Ignoring $xref_id as linkage_annotation has ".$$ignore{$external_db_name}." in it. DELETE THIS MESSAGE AFTER TESTING\n";
next;
}
}
push @transcript_xrefs, $xref_id;
if(!defined($qid) || !defined($tid)){
print "DEPENDENT $xref_id\n" if($ex_db_id != 1100); #HGNC has added one with no %ids.
$percent_id{$xref_id} = 0;
}
else{
$percent_id{$xref_id} = $qid + $tid;
}
$level_db{$xref_id} = $level{$ex_db_id};
}
}
$direct_sth->execute($type, $ens_id ) || die "execute failed";
$direct_sth->bind_columns(\$xref_id, \$ex_db_id, \$display_label,
\$external_db_name, \$linkage_annotation);
while($direct_sth->fetch()){
if($level{$ex_db_id} and $display_label =~ /\D+/){
if(defined($$ignore{$external_db_name})){
if($linkage_annotation =~ /$$ignore{$external_db_name}/){
# print "Ignoring $xref_id as linkage_annotation has ".$$ignore{$external_db_name}." in it. DELETE THIS MESSAGE AFTER TESTING\n";
next;
}
}
push @transcript_xrefs, $xref_id;
$percent_id{$xref_id} = 0;
$level_db{$xref_id} = $level{$ex_db_id};
}
}
}
my $best_tran_xref = 0; # store xref
my $best_tran_level = 0; # store level
my $best_tran_percent = 0; # store best %id total
foreach my $xref_id (@transcript_xrefs) {
if(defined($level_db{$xref_id}) and $level_db{$xref_id}){
if($level_db{$xref_id} < $best_tran_level){
next;
}
if($level_db{$xref_id} == $best_tran_level){
if($percent_id{$xref_id} < $best_tran_percent){
next;
}
}
$best_tran_percent = $percent_id{$xref_id};
$best_tran_level = $level_db{$xref_id};
$best_tran_xref = $xref_id;
}
}
if($best_tran_xref){
print TRANSCRIPT_DX "UPDATE transcript SET display_xref_id=" .$best_tran_xref.
" WHERE transcript_id=" . $transcript_id . ";\n";
print TRANSCRIPT_DX_TXT $best_tran_xref. "\t" . $transcript_id . "\n";
}
if($best_tran_level < $best_gene_level){
next;
}
if($best_tran_level == $best_gene_level){
if($best_tran_percent < $best_gene_percent){
next;
}
}
}
}
close TRANSCRIPT_DX;
close TRANSCRIPT_DX_TXT;
close GENE_DX;
close GENE_DX_TXT;
return @files;
}
sub build_genes_to_transcripts {
my ($self) = @_;
my $sql = "SELECT gene_id, transcript_id, seq_region_start, seq_region_end FROM transcript";
my $sth = $self->core->dbc->prepare($sql);
$sth->execute();
my ($gene_id, $transcript_id, $start, $end);
$sth->bind_columns(\$gene_id, \$transcript_id, \$start, \$end);
# Note %genes_to_transcripts is global
while ($sth->fetch()) {
push @{$genes_to_transcripts{$gene_id}}, $transcript_id;
$transcript_length{$transcript_id} = $end- $start;
}
}
sub load_translation_to_transcript{
my ($self) = @_;
my $sth = $self->core->dbc->prepare("SELECT translation_id, transcript_id FROM translation");
$sth->execute();
my ($translation_id, $transcript_id);
$sth->bind_columns(\$translation_id, \$transcript_id);
while ($sth->fetch()) {
$translation_to_transcript{$translation_id} = $transcript_id;
$transcript_to_translation{$transcript_id} = $translation_id if ($translation_id);
}
}
sub gene_description_sources {
return (
"FlyBaseName_gene",
# "gadfly_gene_cgid",
"FlyBaseCGID_gene",
);
}
sub transcript_display_xref_sources {
my @list = qw(FlyBaseName_transcript FlyBaseCGID_transcript);
# gadfly_transcript_cgid flybase_annotation_id
my %ignore;
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
return [\@list,\%ignore];
}
1;
]]>