From 55dce2ed2b8f4c3d4da552c782baee0ef1349b5a Mon Sep 17 00:00:00 2001
From: Will Spooner <whs@sanger.ac.uk>
Date: Thu, 14 Jun 2007 14:49:27 +0000
Subject: [PATCH] Reimplemented the dump_interpro method so that it dumps any
xrefs, object_xrefs and go_xrefs that may be dependent on the interpro xrefs
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 126 +++++++++++++++---
1 file changed, 108 insertions(+), 18 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index b49bca5fd5..2f1c7ee19e 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -228,6 +228,7 @@ sub build_list_and_map {
my @list=();
my $i = 0;
+
foreach my $method (@{$self->method()}){
my @dna=();
my $q_dna_file = $self->xref->dir."/xref_".$i."_dna.fasta";
@@ -248,7 +249,6 @@ sub build_list_and_map {
}
$i++;
}
-
$self->run_mapping(\@list);
}
@@ -376,7 +376,6 @@ sub dump_xref{
}
my @method=();
-
my @lists =@{$self->get_set_lists()};
my $i=0;
@@ -1243,18 +1242,20 @@ sub parse_mappings {
}
# write relevant xrefs to file
- $max_object_xref_id = $self->dump_core_xrefs(\%primary_xref_ids, $max_object_xref_id, $xref_id_offset);
-
- # dump interpro table as well
- $self->dump_interpro();
+ $max_object_xref_id
+ = $self->dump_core_xrefs(\%primary_xref_ids,
+ $max_object_xref_id, $xref_id_offset);
# dump direct xrefs
- $self->dump_direct_xrefs($xref_id_offset, $max_object_xref_id);
+ $max_object_xref_id
+ = $self->dump_direct_xrefs($xref_id_offset, $max_object_xref_id);
- # dump xrefs that don't appear in either the primary_xref or dependent_xref tables
+ # dump xrefs that don't appear in primary_xref, direct_xref or
+ # dependent_xref tables (e.g. interpro)
$self->dump_orphan_xrefs($xref_id_offset);
-
+ # dump interpro table as well
+ $self->dump_interpro($xref_id_offset,$max_object_xref_id);
}
@@ -2050,31 +2051,120 @@ XSQL
$xref_sth->finish();
print " Wrote $count direct xrefs\n";
-
+ return $object_xref_id;
}
# Dump the interpro table from the xref database
sub dump_interpro {
-
my $self = shift;
+ my $xref_id_offset = shift;
+ my $oxref_id_offset = shift;
- open (INTERPRO, ">" . $self->core->dir() . "/interpro.txt");
+ print "Writing InterPro\n";
+ my( $ipro_count, $xref_count, $oxref_count, $goxref_count ) = (0,0,0,0);
- my $sth = $self->xref->dbc->prepare("SELECT * FROM interpro");
- $sth->execute();
+ open (INTERPRO, ">" . $self->core->dir() . "/interpro.txt");
+ open (XREF, ">>" . $self->core->dir() . "/xref.txt");
+ open (OBJECT_XREF, ">>" . $self->core->dir() . "/object_xref.txt");
+ open (GO_XREF, ">>" . $self->core->dir() . "/go_xref.txt");
+
+ # Get a mapping of protein domains to ensembl translations for
+ # interpro dependent xrefs
+ my $core_sql = "SELECT hit_id, translation_id FROM protein_feature" ;
+ my $core_sth = $self->core->dbc->prepare($core_sql);
+ $core_sth->execute();
+ my %domain_to_translation = ();
+ my ($domain, $translation);
+ $core_sth->bind_columns(\$domain, \$translation);
+ while ($core_sth->fetch()) {
+ $domain_to_translation{$domain} ||= [];
+ push @{$domain_to_translation{$domain}}, $translation;
+ }
- my ($interpro, $pfam);
- $sth->bind_columns(\$interpro, \$pfam);
- while ($sth->fetch()) {
- print INTERPRO $interpro . "\t" . $pfam . "\n";
+ # Get a list of interpro data, including dependent xrefs if avail
+ my $sth = $self->xref->dbc->prepare("
+ SELECT ip.interpro, ip.pfam, x2.xref_id, x2.source_id,
+ x2.accession, x2.version, x2.label, x2.description,
+ dx.linkage_annotation
+ FROM interpro ip, xref x
+ LEFT JOIN dependent_xref dx ON x.xref_id=dx.master_xref_id
+ LEFT JOIN xref x2 ON dx.dependent_xref_id=x2.xref_id
+ WHERE ip.interpro = x.accession");
+ my $rv = $sth->execute();
+ my %interpro_cache;
+ my %xref_cache;
+ my %oxref_cache;
+ my %goxref_cache;
+ while( my $row = $sth->fetchrow_arrayref() ){
+ my ( $interpro, $pfam, $dx_xref_id, $dx_source_id, $dx_accession,
+ $dx_version, $dx_label, $dx_description, $go_linkage ) = @$row;
+ unless( $interpro_cache{$interpro.$pfam} ){
+ # We have a fresh interpro.
+ # Note; interpro xrefs themselves are handled by dump_orphan_xrefs
+ print INTERPRO $interpro . "\t" . $pfam . "\n";
+ $interpro_cache{$interpro.$pfam} ++;
+ $ipro_count++;
+ }
+ if( $dx_accession ){
+ # We have a dependent xref for this interpro...
+ my $xref_id;
+ unless( $xref_id = $xref_cache{$dx_accession} ){
+ $xref_id = $dx_xref_id + $xref_id_offset;
+ $xref_cache{$dx_accession} = $xref_id;
+ printf XREF ("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
+ $xref_id,
+ $source_to_external_db{$dx_source_id},
+ $dx_accession,
+ $dx_label,
+ $dx_version,
+ $dx_description,
+ 'DEPENDENT',
+ "Generated via $interpro");
+ $xref_count++;
+ }
+ foreach my $ensembl_id( @{$domain_to_translation{$pfam}||[]} ){
+ #...And the interpro domain maps to a translation
+ my $oxref_id;
+ 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",
+ $oxref_id,
+ $ensembl_id,
+ 'Translation',
+ $xref_id );
+ $oxref_count ++;
+ }
+ if( $go_linkage ){
+ #...And we have linkage data, indicating a GO sref
+ unless( $goxref_cache{$oxref_id.$go_linkage} ){
+ $goxref_cache{$oxref_id.$go_linkage} ++;
+ printf GO_XREF ( "%s\t%s\n",
+ $oxref_id,
+ $go_linkage );
+ $goxref_count ++;
+ }
+ }
+ }
+ }
}
$sth->finish();
close (INTERPRO);
+ close (XREF);
+ close (OBJECT_XREF);
+ close (GO_XREF);
+ print(" Wrote $ipro_count interpro table entries\n");
+ print(" Wrote $xref_count interpro-dependent xrefs \n");
+ print(" including $oxref_count object xrefs, \n");
+ print(" and $goxref_count go xrefs\n");
+
+ return $oxref_id_offset + $oxref_count;
}
+
sub build_stable_id_to_internal_id_hash {
my ($self) = @_;
--
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