diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 226fcc98a1f4adff0e456733c30cea72ec089d61..0b07d4739ac13c58f1e1b9e8b10c4c324c644c1c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1110,7 +1110,7 @@ sub dump_triage_data() {
my $primary_sql= (<<PSQL);
- SELECT DISTINCT(s.source_id),px.sequence_type
+ SELECT DISTINCT(s.source_id), px.sequence_type
FROM source s, primary_xref px, xref x
WHERE x.xref_id = px.xref_id
AND s.source_id = x.source_id
@@ -1142,7 +1142,7 @@ PSQL
my $summary_failed = "Failed to match at thresholds";
my $summary_missed = "Failed to match";
- my $description_missed = "Unable to match to any ensembl entity at all ";
+ my $description_missed = "Unable to match to any ensembl entity at all";
my $sth = $self->core->dbc->prepare("select MAX(unmapped_reason_id) ".
"from unmapped_reason");
@@ -1188,8 +1188,7 @@ PSQL
}
$sth->finish;
- $sth = $self->core->dbc->prepare("select unmapped_reason_id from unmapped_reason where full_description like '".
- $description_missed."'");
+ $sth = $self->core->dbc->prepare("select unmapped_reason_id from unmapped_reason where full_description like '".$description_missed."'");
$sth->execute();
my $xref_missed_id=undef;
$sth->bind_columns(\$xref_missed_id);
@@ -1266,7 +1265,7 @@ PSQL
print UNMAPPED_OBJECT $xref_DNA_analysis."\t";
}
print UNMAPPED_OBJECT $external_db_id."\t".$accession."\t";
- print UNMAPPED_OBJECT $xref_missed_id."\t0\t0\t\0\tNULL\n"
+ print UNMAPPED_OBJECT $xref_missed_id."\t0\t0\t0\tNULL\n"
}
}
}
@@ -2973,7 +2972,7 @@ sub add_missing_pairs{
# print "xref offset => $xref_id_offset\n";
# print "max object xref => $max_object_xref_id \n";
my $xref_sql = (<<EOS);
- SELECT x1.xref_id, x2.xref_id
+ SELECT x1.xref_id, x2.xref_id, x1.accession, x2.accession
FROM pairs p, xref x1, xref x2
WHERE p.accession1 = x1.accession
AND p.accession2 = x2.accession
@@ -2981,10 +2980,11 @@ sub add_missing_pairs{
EOS
my $xref_sth = $self->xref->dbc->prepare($xref_sql);
$xref_sth->execute();
- my ($xref_id1,$xref_id2);
- $xref_sth->bind_columns(\$xref_id1, \$xref_id2);
+ my ($xref_id1,$xref_id2, $x1_acc, $x2_acc);
+ $xref_sth->bind_columns(\$xref_id1, \$xref_id2, \$x1_acc, \$x2_acc);
my %good2missed=();
+ my %good2missed_acc=();
my $okay =0;
my $both = 0;
my $poss = 0;
@@ -2996,10 +2996,12 @@ EOS
elsif(!defined($xrefs_written{$xref_id2})){
$poss++;
$good2missed{$xref_id1+$xref_id_offset} = $xref_id2+$xref_id_offset;
+ $good2missed_acc{$xref_id1+$xref_id_offset} = $x2_acc;
}
else{
$poss++;
$good2missed{$xref_id2+$xref_id_offset} = $xref_id1+$xref_id_offset;
+ $good2missed_acc{$xref_id2+$xref_id_offset} = $x1_acc;
}
}
else{
@@ -3024,37 +3026,49 @@ EOS
# print "but apparently $okay have no matches at all and $both have two\n";
# print "potential filler ins = $poss\n";
# print "good2missed=>".scalar(%good2missed)."\n";
- open(OBJECT_XREF2, ">".$self->core->dir()."/pairs_object_xref.txt") || die "Could not open pairs_object_xref.txt";
+ open(OBJECT_XREF2, ">".$self->core->dir()."/pairs_object_xref.txt")
+ || die "Could not open pairs_object_xref.txt";
+
+ my $triage_file = $self->core->dir()."/triage_update.sql";
+ open(TRIAGE_UPDATE,">".$triage_file)
+ || die "Could not open $triage_file\n";
my $i=0;
my $index;
my $added = 0;
- my $sql = "SELECT xref_id, ensembl_id, ensembl_object_type FROM object_xref WHERE xref_id IN (";
- my ($goodxref, $ens_int_id,$type);
+ my $sql = "SELECT o.xref_id, o.ensembl_id, o.ensembl_object_type, ";
+ $sql .= "x.dbprimary_acc, x.external_db_id ";
+ $sql .= "FROM object_xref o, xref x ";
+ $sql .= "WHERE x.xref_id = o.xref_id AND x.xref_id IN (";
+ my ($goodxref, $ens_int_id, $type, $acc, $ex_db_id);
my @list =();
foreach my $key (keys %good2missed){
if($i > 200){
my $sth_ob = $self->core->dbc->prepare($sql.(join(',',@list)).")") || die @_;
$sth_ob->execute();
- $sth_ob->bind_columns(\$goodxref,\$ens_int_id,\$type);
+ $sth_ob->bind_columns(\$goodxref,\$ens_int_id,\$type, \$acc, \$ex_db_id);
while($sth_ob->fetch()){
if(($type =~ /Transcript/) and defined($transcript_2_translation{$ens_int_id})){
$max_object_xref_id++;
$added++;
print OBJECT_XREF2 "$max_object_xref_id\t";
- print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\tDEPENDENT\n";
+ print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
+ print TRIAGE_UPDATE "WHERE identifier like '".$good2missed_acc{$goodxref}."' ";
+ print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
}
elsif(($type =~ /Translation/) and defined($translation_2_transcript{$ens_int_id})){
$max_object_xref_id++;
$added++;
print OBJECT_XREF2 "$max_object_xref_id\t";
- print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\tDEPENDENT\n";
+ print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
+ print TRIAGE_UPDATE "WHERE identifier like '".$good2missed_acc{$goodxref}."' ";
+ print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
}
}
$sth_ob->finish();
@@ -3069,25 +3083,29 @@ EOS
if($i){
my $sth_ob = $self->core->dbc->prepare($sql.(join(',',@list)).")") || die @_;
$sth_ob->execute();
- $sth_ob->bind_columns(\$goodxref,\$ens_int_id,\$type);
+ $sth_ob->bind_columns(\$goodxref,\$ens_int_id,\$type, \$acc, \$ex_db_id);
while($sth_ob->fetch()){
if(($type =~ /Transcript/) and defined($transcript_2_translation{$ens_int_id})){
$max_object_xref_id++;
$added++;
print OBJECT_XREF2 "$max_object_xref_id\t";
- print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\tDEPENDENT\n";
+ print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
+ print TRIAGE_UPDATE "WHERE identifier like '".$good2missed_acc{$goodxref}."' ";
+ print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
}
elsif(($type =~ /Translation/) and defined($translation_2_transcript{$ens_int_id})){
$max_object_xref_id++;
$added++;
print OBJECT_XREF2 "$max_object_xref_id\t";
- print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\tDEPENDENT\n";
+ print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
+ print TRIAGE_UPDATE "WHERE identifier like '".$good2missed_acc{$goodxref}."' ";
+ print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
}
}
$sth_ob->finish();
@@ -3108,6 +3126,13 @@ EOS
print "$added new object xrefs added based on the Pairs\n";
+ my $core_db = $self->core->dbc;
+
+ my $str = "mysql -u " .$core_db->username() ." -p" . $core_db->password() .
+ " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < ". $triage_file;
+ system $str;
+
+ print "updated triage data accordingly\n";
}
sub dump_all_dependencies{