diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 2f1c7ee19e907649c6173cbf57880a213b334c35..6270e1dfe4dae488831fefc02f3f1e0a7fb58663 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -81,8 +81,26 @@ my %object_xrefs_written; # Needed in case an xref if matched to one enem
my %failed_xref_mappings;
my %updated_source;
my %XXXxref_id_to_accession;
+my %XXXxref_id_to_source_id;
+my %xref_source_id_to_name;
+sub create_source_id_to_source_name{
+ my($self) = @_;
+ my $sql = (<<SQL);
+ SELECT DISTINCT(source.source_id), source.name
+ FROM source, xref
+ WHERE xref.source_id = source.source_id
+SQL
+
+ my $sth = $self->xref->dbc->prepare($sql);
+ $sth->execute();
+ my ($source_id, $name, $priority);
+ $sth->bind_columns(\$source_id,\$name);
+ while($sth->fetch()){
+ $xref_source_id_to_name{$source_id} = $name;
+ }
+}
=head2 find_priority_sources
@@ -1183,7 +1201,7 @@ sub parse_mappings {
}
# note we add on $xref_id_offset to avoid clashes
$object_succesfully_mapped{query_id} = 1;
- print OBJECT_XREF "$max_object_xref_id\t$target_id\t$type\t" . ($query_id+$xref_id_offset) . "\n";
+ print OBJECT_XREF "$max_object_xref_id\t$target_id\t$type\t" . ($query_id+$xref_id_offset) . "\t\\N\n";
my $identity_string = join("\t", ($query_identity, $target_identity, $query_start+1, $query_end, $target_start+1, $target_end, $cigar_line, $score, "\\N", $analysis_id)) . "\n";
@@ -1331,18 +1349,20 @@ PSQL
print "No accession for ".($xref_id+$xref_id_offset)."\t1\n";
}
$XXXxref_id_to_accession{$xref_id} = $acc;
+#PROCESS PRIORITY XREFS
$dep_list = $self->dump_all_dependencies($xref_id, $xref_id_offset, $type, $id);
push @xref_list, $xref_id;
if(defined($priority_object_xref{$key})){
$object_succesfully_mapped{$xref_id} = 1;
- print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".($xref_id+$xref_id_offset)."\n";
+ print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".($xref_id+$xref_id_offset)."\t\\N\n";
if(defined($priority_identity_xref{$key})){
print IDENTITY_XREF_P $object_xref_id."\t".$priority_identity_xref{$key};
}
$object_xref_id++;
foreach my $dependent (@$dep_list){
$object_succesfully_mapped{$xref_id} = 1;
- print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".$dependent."\n";
+ print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".$dependent.
+ "\tFROM:".$source_name.":".$acc."\n";
print IDENTITY_XREF_TEMP $object_xref_id."\t".$primary_identity{$xref_id};
$object_xref_id++;
}
@@ -1360,7 +1380,7 @@ PSQL
if(defined($priority_object_xref{$key})){
my ($type,$id) = split(/:/,$priority_object_xref{$key});
$object_succesfully_mapped{$xref_id} = 1;
- print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".($xref_id+$xref_id_offset)."\n";
+ print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".($xref_id+$xref_id_offset)."\t\\N\n";
if(defined($priority_identity_xref{$key})){
print IDENTITY_XREF_P $object_xref_id."\t".$priority_identity_xref{$key};
}
@@ -1640,6 +1660,7 @@ PSQL
#dump out dependencies aswell
$XXXxref_id_to_accession{$xref_id} = $accession;
+ $XXXxref_id_to_source_id{$xref_id} = $source_id;
if(!defined($accession) or $accession eq ""){
print STDERR "No accession for ".($xref_id+$xref_id_offset)."\t2\n";
}
@@ -1955,7 +1976,7 @@ XSQL
$xrefs_written{$xref_id} = 1;
}
$object_succesfully_mapped{$xref_id} = 1;
- print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t" . ucfirst($type) . "\t" . ($xref_id+$xref_id_offset) . "\n";
+ print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t" . ucfirst($type) . "\t" . ($xref_id+$xref_id_offset) . "\t\\N\n";
$object_xref_id++;
$count++;
@@ -2013,7 +2034,7 @@ XSQL
}
$ensembl_internal_id = $stable_id_to_internal_id{$type}->{$stable_id};
$object_succesfully_mapped{$xref_id} = 1;
- print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t" . ucfirst($type) . "\t" . ($xref_id+$xref_id_offset) . "\n";
+ print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t" . ucfirst($type) . "\t" . ($xref_id+$xref_id_offset) . "\t\\N\n";
if( $source_id == $go_source_id){
print GO_XREF $object_xref_id . "\t" . $linkage_xref . "\n";
}
@@ -2129,7 +2150,7 @@ sub dump_interpro {
unless( $oxref_id = $oxref_cache{$dx_accession.$ensembl_id} ){
$oxref_id = $oxref_count + 1 + $oxref_id_offset;
$oxref_cache{$dx_accession.$ensembl_id} = $oxref_id;
- printf OBJECT_XREF ( "%s\t%s\t%s\t%s\n",
+ printf OBJECT_XREF ( "%s\t%s\t%s\t%s\t\\N\n",
$oxref_id,
$ensembl_id,
'Translation',
@@ -2301,6 +2322,7 @@ sub dump_core_xrefs {
my %xref_to_objects = %$xref_ids_hashref;
+ $self->create_source_id_to_source_name();
my $dir = $self->core->dir();
open (XREF, ">$dir/xref.txt");
@@ -2375,7 +2397,7 @@ sub dump_core_xrefs {
print " No accession for $xref_id, $accession, $label, $source_id\t3\n";
}
$XXXxref_id_to_accession{$xref_id} = $accession;
-
+ $XXXxref_id_to_source_id{$xref_id} = $source_id;
# make sure label is set to /something/ so that the website displays something
$label = $accession if (!$label);
@@ -2420,12 +2442,18 @@ sub dump_core_xrefs {
$label = $accession if (!$label);
-
my $master_accession = $XXXxref_id_to_accession{$master_xref_id};
-
+# my $master_source_name = $xref_source_id_to_name{$source_id};
+ my $master_source_name = $xref_source_id_to_name{$XXXxref_id_to_source_id{$master_xref_id}};
+
+#IANL need to add source here to be able to add this to object_xref;
+
if(!defined($master_accession) or $master_accession eq ""){
print "(dump_core_xrefs) No master_acc for master xref $master_xref_id,".($master_xref_id+$xref_id_offset)." for $accession ($xref_id)\n";
}
+ if(!defined($master_source_name) or $master_source_name eq ""){
+ print "(dump_core_xrefs) No master_source_name for master xref $master_xref_id,".($master_xref_id+$xref_id_offset)." for $accession ($xref_id)\n";
+ }
if (!$xrefs_written{$xref_id}) {
if(!defined($updated_source{$external_db_id})){
@@ -2485,7 +2513,7 @@ sub dump_core_xrefs {
$object_succesfully_mapped{$xref_id} = 1;
- print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\n";
+ print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tFROM:".$master_source_name.":".$master_accession."\n";
print IDENTITY_XREF $object_xref_id."\t".$primary_identity{$master_xref_id};
# Add this mapping to the list - note NON-OFFSET xref_id is used
@@ -2575,14 +2603,17 @@ sub build_transcript_and_gene_display_xrefs {
print "NO file or zero size file, so not able to load file $file to identity_xref_temp\n";
}
+ #
+ # get a list of sources to use
+ # and also a list of those xrefs to ignore
+ # where the source name is the key and the value is the string to test for
+ #
+ my ($presedence, $ignore) = @{$self->transcript_display_xref_sources()};
-
-
- my @presedence = $self->transcript_display_xref_sources();
my $i=0;
my %level;
- foreach my $ord (reverse (@presedence)){
+ foreach my $ord (reverse (@$presedence)){
$i++;
if(!defined($external_name_to_id{$ord})){
print STDERR "unknown external database name *$ord* being used\n";
@@ -2601,11 +2632,12 @@ sub build_transcript_and_gene_display_xrefs {
my $sql = (<<ESQL);
- SELECT ox.xref_id, ix.query_identity, ix.target_identity, x.external_db_id, x.display_label
- FROM (object_xref ox, xref x)
+ 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'
+ 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";
@@ -2613,11 +2645,12 @@ ESQL
$sql = (<<ZSQL);
- SELECT ox.xref_id, ix.query_identity, ix.target_identity, x.external_db_id, x.display_label
- FROM (object_xref ox, xref x)
+ 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";
@@ -2625,10 +2658,11 @@ ZSQL
$sql = (<<QSQL);
- SELECT x.xref_id, x.external_db_id, x.display_label
- FROM object_xref o, xref x
+ 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";
@@ -2638,17 +2672,18 @@ QSQL
# get xrefs connect directly to the gene.
$sql = (<<GSQL);
- SELECT x.xref_id, x.external_db_id
- FROM object_xref o, xref x
+ 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, $display_label);
+ my ($xref_id, $qid, $tid, $ex_db_id, $display_label, $external_db_name, $linkage_annotation);
@@ -2666,7 +2701,7 @@ GSQL
my @gene_xrefs = ();
$gene_sth->execute($gene_id) || die "execute failed";
- $gene_sth->bind_columns(\$xref_id, \$ex_db_id);
+ $gene_sth->bind_columns(\$xref_id, \$ex_db_id, \$external_db_name, \$linkage_annotation);
my $best_gene_xref = 0; # store xref
@@ -2674,6 +2709,12 @@ GSQL
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 ".$$ignore{$external_db_name}." in it. DELETE THIS MESSAGE AFTER TESTING\n";
+ next;
+ }
+ }
if($level{$ex_db_id} > $best_gene_level){
$best_gene_xref = $xref_id;
$best_gene_level = $level{$ex_db_id};
@@ -2700,9 +2741,18 @@ GSQL
}
}
$primary_sth->execute($type, $ens_id ) || die "execute failed";
- $primary_sth->bind_columns(\$xref_id, \$qid, \$tid, \$ex_db_id, \$display_label);
+ $primary_sth->bind_columns(\$xref_id, \$qid, \$tid, \$ex_db_id,
+ \$display_label, \$external_db_name,
+ \$linkage_annotation);
while($primary_sth->fetch()){
if($level{$ex_db_id} and $display_label =~ /\D+/ ){ #correct level and label is not just a number
+ if(defined($$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";
@@ -2717,25 +2767,40 @@ GSQL
}
$dependent_sth->execute($type, $ens_id ) || die "execute failed";
- $dependent_sth->bind_columns(\$xref_id, \$qid, \$tid, \$ex_db_id, \$display_label);
+ $dependent_sth->bind_columns(\$xref_id, \$qid, \$tid, \$ex_db_id,
+ \$display_label, \$external_db_name,
+ \$linkage_annotation);
while($dependent_sth->fetch()){
if($level{$ex_db_id} and $display_label =~ /\D+/){
- push @transcript_xrefs, $xref_id;
- if(!defined($qid) || !defined($tid)){
- print "DEPENDENT $xref_id\n";
- $percent_id{$xref_id} = 0;
- }
- else{
- $percent_id{$xref_id} = $qid + $tid;
- }
- $level_db{$xref_id} = $level{$ex_db_id};
- }
+ if(defined($$ignore{$external_db_name})){
+ if($linkage_annotation =~ /$$ignore{$external_db_name}/){
+ print "Ignoring $xref_id as linkage_annotation has ".$$ignore{$external_db_name}." in it. DELETE THIS MESSAGE AFTER TESTING\n";
+ next;
+ }
+ }
+ push @transcript_xrefs, $xref_id;
+ if(!defined($qid) || !defined($tid)){
+ print "DEPENDENT $xref_id\n";
+ $percent_id{$xref_id} = 0;
+ }
+ else{
+ $percent_id{$xref_id} = $qid + $tid;
+ }
+ $level_db{$xref_id} = $level{$ex_db_id};
+ }
}
$direct_sth->execute($type, $ens_id ) || die "execute failed";
- $direct_sth->bind_columns(\$xref_id, \$ex_db_id, \$display_label);
+ $direct_sth->bind_columns(\$xref_id, \$ex_db_id, \$display_label,
+ \$external_db_name, \$linkage_annotation);
while($direct_sth->fetch()){
if($level{$ex_db_id} and $display_label =~ /\D+/){
+ if(defined($$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};
@@ -2806,21 +2871,26 @@ GSQL
sub transcript_display_xref_sources {
- return ('RFAM',
- 'miRBase',
- 'IMGT/GENE_DB',
- 'HUGO',
- 'SGD',
- 'MarkerSymbol',
- 'flybase_symbol',
- 'Anopheles_symbol',
- 'Genoscope_annotated_gene',
- 'Uniprot/SWISSPROT',
- 'Uniprot/Varsplic',
- 'RefSeq_peptide',
- 'RefSeq_dna',
- 'Uniprot/SPTREMBL',
- 'EntrezGene');
+ my @list = qw(RFAM
+ miRBase
+ IMGT/GENE_DB
+ HUGO
+ SGD
+ MarkerSymbol
+ flybase_symbol
+ Anopheles_symbol
+ Genoscope_annotated_gene
+ Uniprot/SWISSPROT
+ Uniprot/Varsplic
+ RefSeq_peptide
+ RefSeq_dna
+ Uniprot/SPTREMBL
+ EntrezGene);
+
+ my %ignore;
+ $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+
+ return [\@list,\%ignore];
}
@@ -3894,7 +3964,7 @@ EOS
print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
- print OBJECT_XREF2 "\n";
+ print OBJECT_XREF2 "\t\\N\n";
push @new_list, $goodxref;
@@ -3926,7 +3996,7 @@ EOS
print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
print OBJECT_XREF2 $xref_id+$xref_id_offset;
- print OBJECT_XREF2 "\n";
+ print OBJECT_XREF2 "\t\\N\n";
push @new_list, $goodxref;
push @{$identity_master_xref_to_object_xref{$goodxref}}, $max_object_xref_id;
@@ -3941,7 +4011,7 @@ EOS
print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
- print OBJECT_XREF2 "\n";
+ print OBJECT_XREF2 "\t\\N\n";
push @new_list, $goodxref;
push @{$identity_master_xref_to_object_xref{$goodxref}}, $max_object_xref_id;
@@ -3970,7 +4040,7 @@ EOS
print OBJECT_XREF2 "$max_object_xref_id\t";
print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
print OBJECT_XREF2 $xref_id+$xref_id_offset;
- print OBJECT_XREF2 "\n";
+ print OBJECT_XREF2 "\\N\n";
push @new_list, $good2missed{$goodxref};
push @{$identity_master_xref_to_object_xref{$goodxref}}, $max_object_xref_id;
@@ -4223,6 +4293,7 @@ PSQL
print "No accession for ".($xref_id+$xref_id_offset)."\t4\n";
}
$XXXxref_id_to_accession{$xref_id} = $accession;
+ $XXXxref_id_to_source_id{$xref_id} = $source_id;
$self->dump_all_dependencies($xref_id, $xref_id_offset);
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
index 5c936253af7d31f7c9e9b96df95100402aad2dd2..5633b45bef30147835d71cff95fbad8f13015d8f 100644
--- a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
@@ -31,16 +31,16 @@ sub gene_description_sources {
sub transcript_display_xref_sources {
- return ('RFAM',
- 'miRBase',
- 'Anopheles_symbol',
- 'Uniprot/SWISSPROT',
- 'Uniprot/Varsplic',
- #'RefSeq_peptide',
- #'RefSeq_dna',
- 'Uniprot/SPTREMBL',
- #'EntrezGene'
- );
+ my @list = qw(RFAM
+ miRBase
+ Anopheles_symbol
+ Uniprot/SWISSPROT
+ Uniprot/Varsplic
+ Uniprot/SPTREMBL);
+
+ my %ignore;
+ return [\@list,\%ignore];
+
}
# regexps to match any descriptons we want to filter out
diff --git a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
index 37debb4fd5886a185e7644004b938dd884cf6a2f..20fb6720607d5951a8712c7f53fd3d6a5b370e56 100644
--- a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
@@ -14,16 +14,20 @@ sub get_set_lists {
sub transcript_display_xref_sources {
- return ('ZFIN_ID',
- 'MarkerSymbol',
- 'flybase_symbol',
- 'Anopheles_symbol',
- 'Genoscope_annotated_gene',
- 'Uniprot/SWISSPROT',
- 'RefSeq_peptide',
- 'RefSeq_dna',
- 'Uniprot/SPTREMBL',
- 'EntrezGene');
+ my @list = qw(ZFIN_ID
+ MarkerSymbol
+ flybase_symbol
+ Anopheles_symbol
+ Genoscope_annotated_gene
+ Uniprot/SWISSPROT
+ RefSeq_peptide
+ RefSeq_dna
+ Uniprot/SPTREMBL
+ EntrezGene);
+
+ my %ignore;
+
+ return [\@list,\%ignore];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm b/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm
index b9a8090a7a8b8caeb6d0106474d31c8658573a3b..784e4ee9c90a18b82a53bbc5aa80c3ee9b757a9d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm
@@ -9,25 +9,29 @@ use vars '@ISA';
# Same as in BasicMapper but Genoscope order reversed.
sub transcript_display_xref_sources {
- return ('Platypus_olfactory_receptor',
- 'Oxford_FGU_Oa_tscript',
- 'Oxford_FGU_Oa_gene',
- 'RFAM',
- 'miRBase',
- 'IMGT/GENE_DB',
- 'HUGO',
- 'SGD',
- 'MarkerSymbol',
- 'flybase_symbol',
- 'Anopheles_symbol',
- 'Genoscope_annotated_gene',
- 'Uniprot/SWISSPROT',
- 'Uniprot/Varsplic',
- 'RefSeq_peptide',
- 'RefSeq_dna',
- 'Uniprot/SPTREMBL',
- 'EntrezGene');
-
+ my @list = qw(Platypus_olfactory_receptor
+ Oxford_FGU_Oa_tscript
+ Oxford_FGU_Oa_gene
+ RFAM
+ miRBase
+ IMGT/GENE_DB
+ HUGO
+ SGD
+ MarkerSymbol
+ flybase_symbol
+ Anopheles_symbol
+ Genoscope_annotated_gene
+ Uniprot/SWISSPROT
+ Uniprot/Varsplic
+ RefSeq_peptide
+ RefSeq_dna
+ Uniprot/SPTREMBL
+ EntrezGene);
+
+ my %ignore;
+ $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+
+ return [\@list,\%ignore];
}
sub gene_description_sources {
diff --git a/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm b/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
index 4d129aea163333f142ba22d7f8f95c471c01623d..fef59adb2350e60689e67b51d6a58f364a561791 100644
--- a/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
@@ -15,20 +15,26 @@ sub get_set_lists {
sub transcript_display_xref_sources {
- return ('RFAM',
- 'miRBase',
- 'HUGO',
- 'RGD',
- 'MarkerSymbol',
- 'flybase_symbol',
- 'Anopheles_symbol',
- 'Genoscope_annotated_gene',
- 'Uniprot/SWISSPROT',
- 'Uniprot/Varsplic',
- 'RefSeq_peptide',
- 'RefSeq_dna',
- 'Uniprot/SPTREMBL',
- 'EntrezGene');
+my @list = qw(RFAM
+ miRBase
+ HUGO
+ RGD
+ MarkerSymbol
+ flybase_symbol
+ Anopheles_symbol
+ Genoscope_annotated_gene
+ Uniprot/SWISSPROT
+ Uniprot/Varsplic
+ RefSeq_peptide
+ RefSeq_dna
+ Uniprot/SPTREMBL
+ EntrezGene);
+
+
+ my %ignore;
+ $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+
+ return [\@list,\%ignore];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm b/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm
index c4425f8bf94f605f185a5b4c439130485e16be02..17a7bcb450980e2c9769024b496a5a5f034a2ef4 100644
--- a/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm
@@ -10,17 +10,22 @@ use vars '@ISA';
sub transcript_display_xref_sources {
- return ('HUGO',
- 'MarkerSymbol',
- 'wormbase_transcript',
- 'flybase_symbol',
- 'Anopheles_symbol',
- 'Genoscope_annotated_gene',
- 'Genoscope_predicted_transcript',
- 'Uniprot/SWISSPROT',
- 'RefSeq',
- 'Uniprot/SPTREMBL',
- 'LocusLink');
+ my @list = qw(HUGO
+ MarkerSymbol
+ wormbase_transcript
+ flybase_symbol
+ Anopheles_symbol
+ Genoscope_annotated_gene
+ Genoscope_predicted_transcript
+ Uniprot/SWISSPROT
+ RefSeq
+ Uniprot/SPTREMBL
+ LocusLink);
+
+ my %ignore;
+
+ return [\@list,\%ignore];
+
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm b/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
index dda8b98a5d8a1661da9ab73107af7429e1541fb6..f7e3fb861ef3818372ba6b16e000cc08365e7bf7 100644
--- a/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
@@ -14,17 +14,22 @@ sub get_set_lists{
sub transcript_display_xref_sources {
- return ('Xenopus_Jamboree',
- 'MarkerSymbol',
- 'flybase_symbol',
- 'Anopheles_symbol',
- 'Genoscope_annotated_gene',
- 'Uniprot/SWISSPROT',
- 'RefSeq_peptide',
- 'RefSeq_dna',
- 'Uniprot/SPTREMBL',
- 'EntrezGene');
-
+ my @list = qw(Xenopus_Jamboree
+ MarkerSymbol
+ flybase_symbol
+ Anopheles_symbol
+ Genoscope_annotated_gene
+ Uniprot/SWISSPROT
+ RefSeq_peptide
+ RefSeq_dna
+ Uniprot/SPTREMBL
+ EntrezGene);
+
+
+ my %ignore;
+ $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+
+ return [\@list,\%ignore];
}
1;