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Commit 92a229b9 authored by Glenn Proctor's avatar Glenn Proctor
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Refactoring to allow easier overriding of gene & transcript display_xref setting in subclasses. 

Added "search" for UTR transcripts when generating xref links.
parent 3ab99939
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misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+ 89
− 44
View file @ 92a229b9
......@@ -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
......
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