From 706236ddd84d3ae625c9c94b887f525549becccc Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 27 Jan 2005 09:43:23 +0000
Subject: [PATCH] Now dumps GO linkage types to go_xref and uploads this if
required, allowing display of GO xrefs & related information on website,
assuming ensembl_go database is present and configured.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 34 +++++++++++--------
1 file changed, 20 insertions(+), 14 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 217c249d68..b2ce5625ef 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -729,6 +729,8 @@ sub parse_mappings {
print "Maximum existing object_xref_id = $max_object_xref_id\n";
$max_object_xref_id = 1;
}
+ my $object_xref_id_offset = $max_object_xref_id + 1;
+ my $object_xref_id = $object_xref_id_offset;
$row = @{$self->dbi->selectall_arrayref("SELECT MAX(xref_id) FROM xref")}[0];
my $max_xref_id = @$row[0];
@@ -736,14 +738,10 @@ sub parse_mappings {
print "Can't get highest existing xref_id, using 0\n)";
} else {
print "Maximum existing xref_id = $max_xref_id\n";
- $max_object_xref_id = 1;
+ $object_xref_id_offset = 1;
}
my $xref_id_offset = $max_xref_id + 1;
- #my $ox_sth = $dbi->prepare("INSERT INTO object_xref(ensembl_id, ensembl_object_type, xref_id) VALUES(?,?,?)");
-
- #my $ix_sth = $dbi->prepare("INSERT INTO identity_xref VALUES(?,?,?,?,?,?,?,?,?,?,?)");
-
# files to write table data to
open (OBJECT_XREF, ">$dir/object_xref.txt");
open (IDENTITY_XREF, ">$dir/identity_xref.txt");
@@ -752,8 +750,6 @@ sub parse_mappings {
my $last_lines = 0;
my $total_files = 0;
- my $object_xref_id = $max_object_xref_id + 1;
-
# keep a (unique) list of xref IDs that need to be written out to file as well
# this is a hash of hashes, keyed on xref id that relates xrefs to e! objects (may be 1-many)
my %primary_xref_ids = ();
@@ -837,7 +833,7 @@ sub parse_mappings {
print "Read $total_lines lines from $total_files exonerate output files\n";
# write relevant xrefs to file
- $self->dump_core_xrefs(\%primary_xref_ids, $object_xref_id+1, $xref_id_offset, \%ensembl_object_types);
+ $self->dump_core_xrefs(\%primary_xref_ids, $object_xref_id+1, $xref_id_offset, $object_xref_id_offset, \%ensembl_object_types);
# write comparison info. Can be removed after development
$self->dump_comparison();
@@ -918,7 +914,7 @@ sub get_analysis_id {
sub dump_core_xrefs {
- my ($self, $xref_ids_hashref, $start_object_xref_id, $xref_id_offset, $ensembl_object_types_hashref) = @_;
+ my ($self, $xref_ids_hashref, $start_object_xref_id, $xref_id_offset, $object_xref_id_offset, $ensembl_object_types_hashref) = @_;
my @xref_ids = keys %$xref_ids_hashref;
my %xref_to_objects = %$xref_ids_hashref;
@@ -929,6 +925,7 @@ sub dump_core_xrefs {
open (XREF, ">$dir/xref.txt");
open (OBJECT_XREF, ">>$dir/object_xref.txt");
open (EXTERNAL_SYNONYM, ">$dir/external_synonym.txt");
+ open (GO_XREF, ">$dir/go_xref.txt");
my $xref_dbi = $self->xref()->dbi();
my $core_dbi = $self->dbi();
@@ -970,7 +967,7 @@ sub dump_core_xrefs {
my $xref_sth = $xref_dbi->prepare($sql);
$xref_sth->execute();
- my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id, $master_xref_id);
+ my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id, $master_xref_id, $linkage_annotation);
$xref_sth->bind_columns(\$xref_id, \$accession, \$version, \$label, \$description, \$source_id, \$species_id);
# note the xref_id we write to the file is NOT the one we've just read
@@ -992,12 +989,15 @@ sub dump_core_xrefs {
}
# Now get the dependent xrefs for each of these xrefs and write them as well
- $sql = "SELECT DISTINCT(x.xref_id), dx.master_xref_id, x.accession, x.label, x.description, x.source_id, x.version FROM dependent_xref dx, xref x WHERE x.xref_id=dx.dependent_xref_id AND master_xref_id $id_str";
+ # Store the go_linkage_annotations as we go along (need for dumping go_xref)
+ my $go_source_id = get_source_id_from_source_name($self->xref, "GO");
+
+ $sql = "SELECT DISTINCT(x.xref_id), dx.master_xref_id, x.accession, x.label, x.description, x.source_id, x.version, dx.linkage_annotation FROM dependent_xref dx, xref x WHERE x.xref_id=dx.dependent_xref_id AND master_xref_id $id_str";
my $dep_sth = $xref_dbi->prepare($sql);
$dep_sth->execute();
- $dep_sth->bind_columns(\$xref_id, \$master_xref_id, \$accession, \$label, \$description, \$source_id, \$version);
+ $dep_sth->bind_columns(\$xref_id, \$master_xref_id, \$accession, \$label, \$description, \$source_id, \$version, \$linkage_annotation);
while ($dep_sth->fetch()) {
my $external_db_id = $source_to_external_db{$source_id};
@@ -1021,11 +1021,16 @@ 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";
- $object_xref_id++;
# 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;
+
+ # 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);
+
+ $object_xref_id++;
+
}
}
}
@@ -1051,6 +1056,7 @@ sub dump_core_xrefs {
close(XREF);
close(OBJECT_XREF);
close(EXTERNAL_SYNONYM);
+ close(GO_XREF);
print "Before calling display_xref, object_xref_mappings size " . scalar (keys %object_xref_mappings) . "\n";
@@ -1452,7 +1458,7 @@ sub do_upload {
# TODO warn if table not empty
- foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "gene_description") {
+ foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "gene_description", "go_xref") {
my $file = $self->dir() . "/" . $table . ".txt";
my $sth;
--
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