From efe1fee878911e552c8f8ec5c32b6e77701c0067 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 4 Apr 2005 10:00:20 +0000
Subject: [PATCH] Added searching for unlinked transcripts to deal with
alternaltive UTRs in elegans.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 41 ++++++++++++++-----
1 file changed, 31 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 17a3be17af..c43fbc8e51 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1001,15 +1001,6 @@ 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}) {
@@ -1022,10 +1013,39 @@ sub dump_direct_xrefs {
} else {
- print STDERR "Can't find $type corresponding to stable ID $ensembl_stable_id in ${type}_stable_id, not writing record for xref $accession\n";
+ # deal with UTR transcripts in Elegans and potentially others
+ # Need to link xrefs that are listed as linking to e.g. ZK829.4
+ # to each of ZK829.4.1, ZK829.4.2, ZK829.4.3
+ my $old_object_xref_id = $object_xref_id;
+ if ($source_id == get_source_id_from_source_name($self->xref(), "wormpep_id")) {
+
+ # search for matching stable IDs
+ my $pat = $ensembl_stable_id . '\..+';
+ foreach my $stable_id (keys %{$stable_id_to_internal_id->{$type}}) {
+
+ if ($stable_id =~ /$pat/) {
+
+ if (!$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;
+ }
+ $ensembl_internal_id = $stable_id_to_internal_id->{$type}->{$stable_id};
+ print OBJECT_XREF "$object_xref_id\t$ensembl_internal_id\t" . ucfirst($type) . "\t" . ($xref_id+$xref_id_offset) . "\n";
+ $object_xref_id++;
+
+ }
+
+ } # foreach stable_id
+
+ } # if source_id
+
+ # if we haven't changed $object_xref_id, nothing was written
+ print STDERR "Can't find $type corresponding to stable ID $ensembl_stable_id in ${type}_stable_id, not writing record for xref $accession\n" if ($object_xref_id == $old_object_xref_id);
}
+
+
}
}
@@ -2041,3 +2061,4 @@ sub upload_external_db {
}
1;
+
--
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