From f395526460e0cce46f71bc6a9e33b5b7286a2e1f Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 15 Oct 2004 15:03:59 +0000
Subject: [PATCH] Added storing of ensembl object types for dependent xrefs.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index a0c84dcf0f..ca2754e105 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -694,9 +694,12 @@ sub store {
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 lists, keyed on xref id that relates xrefs to e! objects (may be 1-many)
+ # this is a hash of hashes, keyed on xref id that relates xrefs to e! objects (may be 1-many)
my %primary_xref_ids = ();
+ # also keep track of types of ensembl objects
+ my %ensembl_object_types;
+
my $dir = $self->dir();
foreach my $file (glob("$dir/*.map")) {
@@ -726,6 +729,8 @@ sub store {
# TODO - evalue?
$object_xref_id++;
+ $ensembl_object_types{$target_id} = $type;
+
#push @{$primary_xref_ids{$query_id}}, $target_id;
$primary_xref_ids{$query_id}{$target_id} = $target_id;
@@ -749,7 +754,7 @@ sub store {
print "Read $total_lines lines from $total_files exonerate output files\n";
# write relevant xrefs to file
- $self->dump_xrefs(\%primary_xref_ids, $object_xref_id+1);
+ $self->dump_xrefs(\%primary_xref_ids, $object_xref_id+1, \%ensembl_object_types);
}
@@ -816,9 +821,10 @@ sub get_analysis_id {
sub dump_xrefs {
- my ($self, $xref_ids_hashref, $start_object_xref_id) = @_;
+ my ($self, $xref_ids_hashref, $start_object_xref_id, $ensembl_object_types_hashref) = @_;
my @xref_ids = keys %$xref_ids_hashref;
my %xref_to_objects = %$xref_ids_hashref;
+ my %ensembl_object_types = %$ensembl_object_types_hashref;
open (XREF, ">xref.txt");
open (OBJECT_XREF, ">>object_xref.txt");
@@ -894,9 +900,8 @@ sub dump_xrefs {
if (defined $xref_to_objects{$xref_id}) {
my @objects = keys( %{$xref_to_objects{$xref_id}} );
print "xref $accession has " . scalar(@objects) . " associated ensembl objects\n";
- # TODO type - keep hash in store method?
- my $type = "xxx";
foreach my $object_id (@objects) {
+ my $type = $ensembl_object_types{$object_id};
print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t$core_xref_id DEPENDENT\n";
$object_xref_id++;
}
--
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