From 9d5de234d74b0d8f63b46fc715f1b5079d1cf90b Mon Sep 17 00:00:00 2001
From: Nick Langridge <nickl@ebi.ac.uk>
Date: Thu, 10 May 2012 09:07:55 +0000
Subject: [PATCH] added seq region name
---
.../ebi_search_dump/ebi_search_dump_generic.pl | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl b/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
index de289641a5..6f11bd92f1 100755
--- a/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
+++ b/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
@@ -560,13 +560,14 @@ g.seq_region_id=ae.seq_region_id and ae.exc_type='HAP'", [qw(gene_id)]
'gene_name' => $xref_display_label ? $xref_display_label
: $gene_stable_id,
- 'ana_desc_label' => $analysis_description_display_label,
- 'ad' => $analysis_description,
- 'source' => ucfirst($gene_source),
- 'st' => $gene_status,
- 'biotype' => $gene_biotype,
- 'genomic_unit' => $genomic_unit,
- 'location' => sprintf( '%s:%s-%s', $seq_region_name, $seq_region_start, $seq_region_end ),
+ 'seq_region_name' => $seq_region_name,
+ 'ana_desc_label' => $analysis_description_display_label,
+ 'ad' => $analysis_description,
+ 'source' => ucfirst($gene_source),
+ 'st' => $gene_status,
+ 'biotype' => $gene_biotype,
+ 'genomic_unit' => $genomic_unit,
+ 'location' => sprintf( '%s:%s-%s', $seq_region_name, $seq_region_start, $seq_region_end ),
);
$old{'source'} =~ s/base/Base/;
$old{'exons'} = $exons{$gene_id};
@@ -679,6 +680,7 @@ sub geneLineXML {
or die "external_identifiers not set";
my $description = $xml_data->{'description'};
my $gene_name = $xml_data->{'gene_name'};
+ my $seq_region_name = $xml_data->{'seq_region_name'};
my $type = $xml_data->{'source'} . ' ' . $xml_data->{'biotype'}
or die "problem setting type";
my $haplotype = $xml_data->{'haplotype'};
@@ -822,6 +824,7 @@ sub geneLineXML {
<field name="genomic_unit">$genomic_unit</field>} : '') . qq{
<field name="transcript_count">$transcript_count</field>
<field name="gene_name">$gene_name</field>
+ <field name="seq_region_name">$seq_region_name</field>
<field name="haplotype">$haplotype</field>}
. (
join "",
--
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