diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila.pm
index 712b8a1bd826503464a9533db189857e58ccde2d..efd27f9d35d4677bcefda3fc9a6f896f421c66bb 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila.pm
@@ -53,15 +53,10 @@ sub gene_description_sources {
}
sub transcript_display_xref_sources {
- my $self = shift;
- my $fullmode = shift;
+ my $self = shift;
- my @list = qw(FlyBaseName_transcript
- FlyBaseCGID_transcript);
-
- # gadfly_transcript_cgid flybase_annotation_id
-
- print "Get FlyBase Transcript display_xrefs_sources with fullmode=$fullmode\n" if ($self->verbose);
+ my @list = qw(FlyBaseName_transcript
+ FlyBaseCGID_transcript);
my %ignore;
@@ -70,316 +65,20 @@ sub transcript_display_xref_sources {
}
sub gene_display_xref_sources {
- my $self = shift;
- my $fullmode = shift;
+ my $self = shift;
my @list = qw(FlyBaseName_gene
FlyBaseCGID_gene
flybase_gene_id);
my %ignore;
-
- print "Get FlyBase Gene display_xrefs_sources with fullmode=$fullmode\n" if ($self->verbose);
+
return [\@list,\%ignore];
}
-sub set_display_xrefs{
- my $self = shift;
-
- print "Building FlyBase Transcript and Gene display_xrefs using xref database\n" if ($self->verbose);
-
- my $xref_offset = $self->get_meta_value("xref_offset");
-
- print "Using xref_off set of $xref_offset\n" if($self->verbose);
-
- my $reset_sth = $self->core->dbc->prepare("UPDATE gene SET display_xref_id = null");
- $reset_sth->execute();
- $reset_sth->finish;
-
- $reset_sth = $self->core->dbc->prepare("UPDATE transcript SET display_xref_id = null");
- $reset_sth->execute();
- $reset_sth->finish;
-
- my $update_gene_sth = $self->core->dbc->prepare("UPDATE gene g SET g.display_xref_id= ? WHERE g.gene_id=?");
- my $update_tran_sth = $self->core->dbc->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?");
-
- ##############################################
- # Careful: The table might have been created #
- # already if the pipeline was run previously #
- # delete the table first (if not here) #
- ##############################################
-
- my $sth = $self->xref->dbc->prepare("DROP TABLE IF EXISTS display_xref_prioritys");
- $sth->execute;
- $sth->finish;
-
-my $sql =(<<SQL);
- CREATE TABLE display_xref_prioritys(
- source_id INT NOT NULL,
- priority INT NOT NULL,
- PRIMARY KEY (source_id)
- ) COLLATE=latin1_swedish_ci TYPE=InnoDB
-SQL
-
- $sth = $self->xref->dbc->prepare($sql);
- $sth->execute;
- $sth->finish;
-
- ############################################
- # We also create an extra table for the #
- # gene priority #
- ############################################
-
- my $sth = $self->xref->dbc->prepare("DROP TABLE IF EXISTS gene_display_xref_prioritys");
- $sth->execute;
- $sth->finish;
-
-my $g_sql =(<<GSQL);
- CREATE TABLE gene_display_xref_prioritys(
- source_id INT NOT NULL,
- priority INT NOT NULL,
- PRIMARY KEY (source_id)
- ) COLLATE=latin1_swedish_ci TYPE=InnoDB
-GSQL
-
- $sth = $self->xref->dbc->prepare($g_sql);
- $sth->execute;
- $sth->finish;
-
- ############################################
- # OK comes the specific code for FlyBase: #
- # Separate Transcript display xrefs from #
- # gene display xrefs. #
- # get a list of sources to use. #
- # Gene and Trans. have different levels: #
- # transcript presedence should never be #
- # mixed with gene presedence #
- # for this reason, we have to create a #
- # distinct gene_level / transcript_level #
- ############################################
-
- # in we are here, it means that fullmode = 1;
- my $fullmode = 1;
- my ($gene_presedence, $gene_ignore) = @{$self->gene_display_xref_sources($fullmode)};
- my ($transcript_presedence, $transcript_ignore) = @{$self->transcript_display_xref_sources($fullmode)};
-
- my $i=0;
- my $j=0;
-
- my $ins_p_sth = $self->xref->dbc->prepare("INSERT into display_xref_prioritys (source_id, priority) values(?, ?)");
- my $ins_g_p_sth = $self->xref->dbc->prepare("INSERT into gene_display_xref_prioritys (source_id, priority) values(?, ?)");
- my $get_source_id_sth = $self->xref->dbc->prepare("select source_id from source where name like ? order by priority desc");
-
- ############################################
- # So the higher the number the better then #
- # Do it for transcripts and then for genes #
- ############################################
-
- my $last_name = "";
- print "Transcript presedence for the display xrefs\n" if($self->verbose);
- foreach my $name (reverse (@$transcript_presedence)){
- $i++;
- $get_source_id_sth->execute($name);
- my $source_id;
- $get_source_id_sth->bind_columns(\$source_id);
- while($get_source_id_sth->fetch){
- $ins_p_sth->execute($source_id, $i);
- if($name ne $last_name){
- print "\t$name\t$i\n" if ($self->verbose);
- }
- $last_name = $name;
- }
- }
- $ins_p_sth->finish;
-
- $last_name = "";
- print "Gene presedence for the display xrefs\n" if($self->verbose);
- foreach my $name (reverse (@$gene_presedence)){
- $j++;
- $get_source_id_sth->execute($name);
- my $source_id;
- $get_source_id_sth->bind_columns(\$source_id);
- while($get_source_id_sth->fetch){
- $ins_g_p_sth->execute($source_id, $j);
- if($name ne $last_name){
- print "\t$name\t$j\n" if ($self->verbose);
- }
- $last_name = $name;
- }
- }
- $ins_p_sth->finish;
-
- $get_source_id_sth->finish;
-
- ############################################
- # Set status to 'NO_DISPLAY' for those that#
- # match the ignore REGEXP in object_xref #
- # Xrefs have already been dump to core etc #
- # so no damage done. #
- ############################################
-
- my $update_ignore_sth = $self->xref->dbc->prepare('UPDATE object_xref SET ox_status = "NO_DISPLAY" where object_xref_id = ?');
-
- ############################################
- # Gene and transcript ignore are the same #
- ############################################
-
- foreach my $ignore_sql (values %$transcript_ignore){
- print "IGNORE SQL: $ignore_sql\n" if($self->verbose);
- my $ignore_sth = $self->xref->dbc->prepare($ignore_sql);
-
- my $gene_count = 0;
- $ignore_sth->execute();
- my ($object_xref_id);
- $ignore_sth->bind_columns(\$object_xref_id);
- while($ignore_sth->fetch()){
- $update_ignore_sth->execute($object_xref_id);
- }
- $ignore_sth->finish;
- }
- $update_ignore_sth->finish;
-
- #
- # Do a similar thing for those with a display_label that is just numeric;
- #
-
- $update_ignore_sth = $self->xref->dbc->prepare('UPDATE object_xref ox, source s, xref x SET ox_status = "NO_DISPLAY" where ox_status like "DUMP_OUT" and s.source_id = x.source_id and x.label REGEXP "^[0-9]+$" and ox.xref_id = x.xref_id');
-
- $update_ignore_sth->execute();
- $update_ignore_sth->finish;
-
-
-#######################################################################
-
-my $display_xref_sql =(<<DXS);
-select IF (ox.ensembl_object_type = 'Gene', gtt_gene.gene_id,
- IF (ox.ensembl_object_type = 'Transcript', gtt_transcript.gene_id,
- gtt_translation.gene_id)) AS gene_id,
- IF (ox.ensembl_object_type = 'Gene', gtt_gene.transcript_id,
- IF (ox.ensembl_object_type = 'Transcript', gtt_transcript.transcript_id,
- gtt_translation.transcript_id)) AS transcript_id,
- p.priority as priority,
- x.xref_id,
- ox.ensembl_object_type as object_type,
- x.label as label
-from ( display_xref_prioritys p
- join ( source s
- join ( xref x
- join ( object_xref ox
- join ( identity_xref ix
- ) using (object_xref_id)
- ) using (xref_id)
- ) using (source_id)
- ) using (source_id)
- )
- left join gene_transcript_translation gtt_gene
- on (gtt_gene.gene_id = ox.ensembl_id)
- left join gene_transcript_translation gtt_transcript
- on (gtt_transcript.transcript_id = ox.ensembl_id)
- left join gene_transcript_translation gtt_translation
- on (gtt_translation.translation_id = ox.ensembl_id)
-where ox.ox_status = 'DUMP_OUT'
-order by gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC, ox.unused_priority DESC
-
-DXS
-
-my $gene_display_xref_sql =(<<G_DXS);
-select gtt_gene.gene_id AS gene_id,
- p.priority as priority,
- x.xref_id,
- ox.ensembl_object_type as object_type,
- x.label as label
-from ( gene_display_xref_prioritys p
- join ( source s
- join ( xref x
- join ( object_xref ox
- join ( identity_xref ix
- ) using (object_xref_id)
- ) using (xref_id)
- ) using (source_id)
- ) using (source_id)
- )
- left join gene_transcript_translation gtt_gene
- on (gtt_gene.gene_id = ox.ensembl_id)
-where ox.ox_status = 'DUMP_OUT'
-and ox.ensembl_object_type = 'Gene'
-order by gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC, ox.unused_priority DESC
-
-G_DXS
-
-
- my $gene_display_xref_sth = $self->xref->dbc->prepare($gene_display_xref_sql);
-
- my $gene_count = 0;
- my $last_gene = 0;
- my $transcript_count = 0;
-
- $gene_display_xref_sth->execute();
-
- my ($gene_id, $transcript_id, $p, $xref_id, $type, $label); # remove labvel after testig it is not needed
- $gene_display_xref_sth->bind_columns(\$gene_id, \$p, \$xref_id, \$type, \$label);
- while($gene_display_xref_sth->fetch()){
- if($gene_id != $last_gene){
- $update_gene_sth->execute($xref_id+$xref_offset, $gene_id);
- $last_gene = $gene_id;
- $gene_count++;
- }
- }
-
- $gene_display_xref_sth->finish;
-
- print "Updated $gene_count display_xrefs for FlyBase genes\n" if($self->verbose);
-
- my %seen_transcript; # first time we see it is the best due to ordering :-)
- # so either write data to database or store
-
- $last_gene = 0;
-
- my $display_xref_sth = $self->xref->dbc->prepare($display_xref_sql);
-
-
- $display_xref_sth->execute();
- $display_xref_sth->bind_columns(\$gene_id, \$transcript_id, \$p, \$xref_id, \$type, \$label);
- while($display_xref_sth->fetch()){
- if($gene_id != $last_gene){
- $last_gene = $gene_id;
- }
- if($type ne "Gene"){
- if(!defined($seen_transcript{$transcript_id})){ # not seen yet so its the best
- $update_tran_sth->execute($xref_id+$xref_offset, $transcript_id);
- }
- $seen_transcript{$transcript_id} = $xref_id+$xref_offset;
- $transcript_count++;
- }
- }
-
- $display_xref_sth->finish;
- $update_gene_sth->finish;
- $update_tran_sth->finish;
-
- #
- # reset the status to DUMP_OUT fro thise that where ignored for the display_xref;
- #
-
- my $reset_status_sth = $self->xref->dbc->prepare('UPDATE object_xref SET ox_status = "DUMP_OUT" where ox_status = "NO_DISPLAY"');
- $reset_status_sth->execute();
- $reset_status_sth->finish;
-
- $sth = $self->xref->dbc->prepare("drop table display_xref_prioritys");
- $sth->execute || die "Could not drop temp table display_xref_prioritys\n";
- $sth->finish;
-
- # also drop the gene_display_xref_prioritys
- $sth = $self->xref->dbc->prepare("drop table gene_display_xref_prioritys");
- $sth->execute || die "Could not drop temp table display_xref_prioritys\n";
- $sth->finish;
-
- print "Updated $transcript_count display_xrefs for FlyBase transcripts\n" if($self->verbose);
-}
-
sub build_genes_to_transcripts {
my ($self) = @_;