From bdf98454dce5bf8f0767d54770d0f91820d17b62 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 3 Feb 2005 09:38:18 +0000
Subject: [PATCH] Added support for dumping & uploading direct_xrefs. Will be
used for CCDS xrefs.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 32 +++++++++++--------
1 file changed, 18 insertions(+), 14 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index c875ce4855..45a1c5090f 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -47,6 +47,8 @@ my %object_xref_identities;
my %xref_descriptions;
my %xref_accessions;
my %source_to_external_db;
+my %xrefs_written;
+my %object_xrefs_written;
=head2 dump_seqs
@@ -873,8 +875,11 @@ sub dump_orphan_xrefs() {
my $external_db_id = $source_to_external_db{$source_id};
if ($external_db_id) { # skip "unknown" sources
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
- $count++;
+ if (!$xrefs_written{$xref_id}) {
+ print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
+ $xrefs_written{$xref_id} = 1;
+ $count++;
+ }
}
}
@@ -895,7 +900,7 @@ sub dump_direct_xrefs {
print "Writing direct xrefs\n";
- my $count;
+ my $count = 0;
open (XREF, ">>" . $self->dir() . "/xref.txt");
open (OBJECT_XREF, ">>" . $self->dir() . "/object_xref.txt");
@@ -912,27 +917,27 @@ sub dump_direct_xrefs {
while ($xref_sth->fetch()) {
my $external_db_id = $source_to_external_db{$source_id};
-
if ($external_db_id) {
# Look up Ensembl internal ID from stable ID. No joins, so quick.
- my $table = lc($type);
- my $core_sql = "SELECT ${table}_id FROM ${table}_stable_id WHERE stable_id=\'$ensembl_stable_id\'" ;
+ my $core_sql = "SELECT ${type}_id FROM ${type}_stable_id WHERE stable_id=\'$ensembl_stable_id\'" ;
my $core_sth = $self->dbi()->prepare($core_sql);
- my $core_sth->execute();
+ $core_sth->execute();
my @row = $core_sth->fetchrow_array();
my $ensembl_internal_id = $row[0];
-
if ($ensembl_internal_id) {
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
- print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t$type\t" . ($xref_id+$xref_id_offset) . "\n";
+ if (!$xrefs_written{$xref_id}) {
+ print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
+ $xrefs_written{$xref_id} = 1;
+ }
+ print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t" . ucfirst($type) . "\t" . ($xref_id+$xref_id_offset) . "\n";
$object_xref_id++;
$count++;
} else {
- print STDERR "Can't find $table corresponding to stable ID $ensembl_stable_id in ${table}_stable_id, not writing record for xref $accession\n";
+ print STDERR "Can't find $type corresponding to stable ID $ensembl_stable_id in ${type}_stable_id, not writing record for xref $accession\n";
}
@@ -1072,10 +1077,9 @@ sub dump_core_xrefs {
# execute several queries with a max of 200 entries in each IN clause - more efficient
my $batch_size = 200;
- # keep track of what xref_id & object_xref_ids have been written to prevent
+ # keep track of what xref_id & object_xref_ids have been written to prevent
# duplicates; e.g. several dependent xrefs may be dependent on the same master xref.
- my %xrefs_written;
- my %object_xrefs_written;
+ # Note %xrefs_written and %object_xrefs_written are global
while(@xref_ids) {
--
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