diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 9234a5f8fadd1f1b226a3341700a502acd168a65..17a3be17af146b8c2df6c2f1eff281331dd6591a 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -791,7 +791,7 @@ sub parse_mappings {
$row = @{$self->dbi->selectall_arrayref("SELECT MAX(xref_id) FROM xref")}[0];
my $max_xref_id = @$row[0];
if (!defined $max_xref_id) {
- print "Can't get highest existing xref_id, using 1\n)";
+ print "Can't get highest existing xref_id, using 1\n";
$max_xref_id = 1;
} else {
print "Maximum existing xref_id = $max_xref_id\n";
@@ -1000,6 +1000,16 @@ sub dump_direct_xrefs {
}
my $ensembl_internal_id = $stable_id_to_internal_id->{$type}->{$ensembl_stable_id};
+
+ # horrible hack to deal with UTR transcripts in Elegans
+ my $postfix = 1;
+ while (!$ensembl_internal_id && $postfix < 5) {
+ my $utr_stable_id = $ensembl_stable_id . ".$postfix" ;
+ $ensembl_internal_id = $stable_id_to_internal_id->{$type}->{$utr_stable_id};
+ $postfix++;
+ }
+ # end horrible hack
+
if ($ensembl_internal_id) {
if (!$xrefs_written{$xref_id}) {
@@ -1255,11 +1265,16 @@ sub dump_core_xrefs {
my $full_key = $type."|".$object_id."|".$xref_id;
if (!$object_xrefs_written{$full_key}) {
print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
+
# Add this mapping to the list - note NON-OFFSET xref_id is used
my $key = $type . "|" . $object_id;
push @{$object_xref_mappings{$key}}, $xref_id;
$object_xrefs_written{$full_key} = 1;
+ # Also store *parent's* query/target identity for dependent xrefs
+ $object_xref_identities{$object_id}->{$xref_id}->{"target_identity"} = $object_xref_identities{$object_id}->{$master_xref_id}->{"target_identity"};
+ $object_xref_identities{$object_id}->{$xref_id}->{"query_identity"} = $object_xref_identities{$object_id}->{$master_xref_id}->{"query_identity"};
+
# write a go_xref with the appropriate linkage type
print GO_XREF $object_xref_id . "\t" . $linkage_annotation . "\n" if ($source_id == $go_source_id);
@@ -1297,7 +1312,12 @@ sub dump_core_xrefs {
# calculate display_xref_ids for transcripts and genes
my $transcript_display_xrefs = $self->build_transcript_display_xrefs($xref_id_offset);
- $self->build_gene_display_xrefs_and_descriptions($transcript_display_xrefs);
+ build_genes_to_transcripts();
+
+ $self->build_gene_display_xrefs($transcript_display_xrefs);
+
+ # now build gene descriptions
+ $self->build_gene_descriptions();
return $object_xref_id;
@@ -1397,15 +1417,34 @@ sub build_transcript_display_xrefs {
# use the one with the highest priority, i.e. lower list position in @priorities
my @xrefs = @{$object_xref_mappings{$key}};
my ($best_xref, $best_xref_priority_idx);
+ # store best query & target identities for each source
+ my %best_qi;
+ my %best_ti;
$best_xref_priority_idx = 99999;
foreach my $xref (@xrefs) {
my $source = $xref_to_source{$xref};
if ($source) {
my $i = find_in_list($source, @priorities);
- if ($i > -1 && $i < $best_xref_priority_idx) {
+
+ my $s = $source . "|" . $xref;
+ my $query_identity = $object_xref_identities{$object_id}->{$xref}->{"query_identity"};
+ my $target_identity = $object_xref_identities{$object_id}->{$xref}->{"target_identity"};
+
+ print "###$type $object_id: xref $xref pri $i qi $query_identity\n" if ((($object_id == 93561 && $type =~ /Transcript/) || ($object_id == 65810 && $type =~ /Translation/)) && $i == 0);
+ print "xref $xref $type $object_id pri $i qi $query_identity best qi " . $best_qi{$s} . " ti $target_identity\n" if ($xref == 397813 || $xref == 397814);
+ # Check if this source has a better priority than the current best one
+ # Note if 2 sources are the same priority, the mappings are compared on
+ # query_identity then target_identity
+# if ($i > -1 && $i < $best_xref_priority_idx &&
+# (($query_identity > $best_query_identity) ||
+# ($query_identity == $best_query_identity && $target_identity > $best_target_identity))) {
+ if ($i > -1 && $i < $best_xref_priority_idx && $query_identity > $best_qi{$s}) {
$best_xref = $xref;
$best_xref_priority_idx = $i;
+ $best_qi{$s} = $query_identity;
+ print "Setting best qi $s to $query_identity\n" if ($xref == 397813 || $xref == 397814);
+ $best_ti{$s} = $target_identity;
}
} else {
warn("Couldn't find a source for xref $xref \n");
@@ -1413,6 +1452,7 @@ sub build_transcript_display_xrefs {
}
# store object type, id, and best xref id and source priority
if ($best_xref) {
+ print "##setting obj to best xref $key to $best_xref | $best_xref_priority_idx\n" if ($best_xref == 397813 || $best_xref == 397814);
$obj_to_best_xref{$key} = $best_xref . "|" . $best_xref_priority_idx;
}
@@ -1439,7 +1479,6 @@ sub build_transcript_display_xrefs {
# If transcript has a translation, use the best xref out of the transcript & translation
-
my $transcript_id;
my $translation_id;
if ($type =~ /Transcript/i) {
@@ -1452,13 +1491,16 @@ sub build_transcript_display_xrefs {
$object_id = $transcript_id;
}
else{
- print "$type type error BARFFF!!!\n";
+ print "Cannot deal with type $type\n";
next;
}
if ($translation_id) {
my ($translation_xref, $translation_priority) = split /\|/, $obj_to_best_xref{"Translation|$translation_id"};
my ($transcript_xref, $transcript_priority) = split /\|/, $obj_to_best_xref{"Transcript|$transcript_id"};
-
+ my $transcript_qi = $object_xref_identities{$object_id}->{$transcript_xref}->{"query_identity"};
+ my $translation_qi = $object_xref_identities{$object_id}->{$translation_xref}->{"query_identity"};
+
+print "translation 65810: translation xref: $translation_xref $translation_priority transcript_xref $transcript_xref $transcript_priority\n" if ($type =~ /Translation/ && $object_id == 65810);
if(!$translation_xref){
$best_xref = $transcript_xref;
$best_xref_priority_idx = $transcript_priority;
@@ -1467,7 +1509,7 @@ sub build_transcript_display_xrefs {
$best_xref = $translation_xref;
$best_xref_priority_idx = $translation_priority;
}
- elsif ($translation_priority < $transcript_priority) {
+ elsif ($translation_priority < $transcript_priority && $translation_qi > $transcript_qi) {
$best_xref = $translation_xref;
$best_xref_priority_idx = $translation_priority;
} else {
@@ -1480,7 +1522,7 @@ sub build_transcript_display_xrefs {
# Write record with xref_id_offset
print TRANSCRIPT_DX "UPDATE transcript SET display_xref_id=" . ($best_xref+$xref_id_offset) . " WHERE transcript_id=" . $object_id . ";\n";
- print "wrote " . $best_xref . " (plus offset) for 95625\n" if ($object_id eq 95625);
+ print "wrote " . $best_xref . " (plus offset) for 93591\n" if ($object_id eq 93591);
print TRANSCRIPT_DX_TXT ($best_xref+$xref_id_offset) . "\t" . $object_id . "\n";
$n++;
@@ -1505,7 +1547,7 @@ sub build_transcript_display_xrefs {
# Gene gets the display xref of the highest priority of all of its transcripts
# If more than one transcript with the same priority, longer transcript is used
-sub build_gene_display_xrefs_and_descriptions {
+sub build_gene_display_xrefs {
my ($self, $transcript_display_xrefs) = @_;
@@ -1520,23 +1562,6 @@ sub build_gene_display_xrefs_and_descriptions {
-group => 'core');
my $ta = $db->get_TranscriptAdaptor();
- print "Building gene display_xrefs\n";
- print "Getting transcripts for all genes\n";
-
- my $sql = "SELECT gene_id, transcript_id FROM transcript";
- my $sth = $core_dbi->prepare($sql);
- $sth->execute();
-
- my ($gene_id, $transcript_id);
- $sth->bind_columns(\$gene_id, \$transcript_id);
-
- # Note %genes_to_transcripts is global
- while ($sth->fetch()) {
- push @{$genes_to_transcripts{$gene_id}}, $transcript_id;
- }
-
- print "Got " . scalar keys(%genes_to_transcripts) . " genes\n";
-
print "Assigning display_xrefs to genes\n";
open (GENE_DX, ">$dir/gene_display_xref.sql");
@@ -1599,8 +1624,7 @@ sub build_gene_display_xrefs_and_descriptions {
print "Couldn't find display_xrefs for $miss genes\n" if ($miss > 0);
print "Found display_xrefs for all genes\n" if ($miss eq 0);
- # now build gene descriptions
- $self->build_gene_descriptions(\%genes_to_transcripts);
+ return \%genes_to_transcripts;
}
@@ -1611,7 +1635,7 @@ sub transcript_display_xref_sources {
return ('HUGO',
'MarkerSymbol',
- 'wormbase_transcript',
+# 'wormbase_transcript',
'flybase_symbol',
'Anopheles_symbol',
'Genoscope_annotated_gene',
@@ -1625,6 +1649,29 @@ sub transcript_display_xref_sources {
}
+# Get transcripts associated with each gene
+
+sub build_genes_to_transcripts {
+
+ my ($self) = @_;
+
+ print "Getting transcripts for all genes\n";
+
+ my $sql = "SELECT gene_id, transcript_id FROM transcript";
+ my $sth = $core_dbi->prepare($sql);
+ $sth->execute();
+
+ my ($gene_id, $transcript_id);
+ $sth->bind_columns(\$gene_id, \$transcript_id);
+
+ # Note %genes_to_transcripts is global
+ while ($sth->fetch()) {
+ push @{$genes_to_transcripts{$gene_id}}, $transcript_id;
+ }
+
+ print "Got " . scalar keys(%genes_to_transcripts) . " genes\n";
+
+}
# Find the index of an item in a list(ref), or -1 if it's not in the list.
# Only look for exact matches (case insensitive)
@@ -1728,7 +1775,7 @@ sub do_upload {
}
# don't seem to be able to use prepared statements here
- $sth = $core_dbi->prepare("LOAD DATA INFILE \'$file\' INTO TABLE $table");
+ $sth = $core_dbi->prepare("LOAD DATA INFILE \'$file\' IGNORE INTO TABLE $table");
print "Uploading data in $file to $table\n";
$sth->execute();
@@ -1737,7 +1784,7 @@ sub do_upload {
# gene_display_xref.sql etc
foreach my $table ("gene", "transcript") {
- my $file = $self->dir() . "/" . $table . "_display_xref.txt";
+ my $file = $self->dir() . "/" . $table . "_display_xref.sql";
my $sth;
if ($deleteexisting) {
@@ -1749,18 +1796,16 @@ sub do_upload {
}
print "Setting $table display_xrefs from $file\n";
- # TODO this better
- #my $str = "mysql -u " .$self->user() ." -p" . $self->password() . " -h " . $self->host() ." -P " . $self->port() . " " .$self->dbname() . " < $file";
- #system $str;
-
- $sth = $core_dbi->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
- open(DX_TXT, $file);
- while (<DX_TXT>) {
- my ($xref_id, $object_id) = split;
- $sth->execute($xref_id, $object_id);
- }
-
- close(DX_TXT);
+ my $str = "mysql -u " .$self->user() ." -p" . $self->password() . " -h " . $self->host() ." -P " . $self->port() . " " .$self->dbname() . " < $file";
+ system $str;
+
+ #$sth = $core_dbi->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
+ #open(DX_TXT, $file);
+ #while (<DX_TXT>) {
+ # my ($xref_id, $object_id) = split;
+ # $sth->execute($xref_id, $object_id);
+ #}
+ #close(DX_TXT);
}
}
@@ -1792,7 +1837,7 @@ sub do_upload {
sub build_gene_descriptions {
- my ($self, $genes_to_transcripts) = @_;
+ my ($self) = @_;
# TODO - don't call this from, but after, gene_display_xref