From 84613cc46f7e1110d6df14687744692a45e708f9 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 22 Sep 2005 14:29:58 +0000
Subject: [PATCH] Now parses cg_name=XXX parts of header and creates
dependent_xrefs to Celera_Genes.
---
.../xref_mapping/XrefParser/CeleraParser.pm | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
index 73ec696c83..6d809f6ab0 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
@@ -21,6 +21,8 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
+ my $celera_gene_source_id = $self->get_source_id_for_source_name('Celera_Gene');
+
my @xrefs;
local $/ = "\n>";
@@ -36,7 +38,7 @@ sub run {
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
# deconstruct header - just use first part
- my ($accession, @rest) = split /,/, $header;
+ my ($accession, $cg) = split /,/, $header;
# make sequence into one long string
$sequence =~ s/\n//g;
@@ -50,6 +52,17 @@ sub run {
$xref->{SEQUENCE_TYPE} = $self->get_sequence_type();
$xref->{STATUS} = 'experimental';
+ # pull cg_name from peptide files as well and create dependent xrefs
+ if ($self->get_sequence_type() =~ /peptide/) {
+ my ($cg_name) = $cg =~ /cg_name=(.*)/;
+ my %dep;
+ $dep{SOURCE_NAME} = 'Celera_Gene';
+ $dep{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
+ $dep{SOURCE_ID} = $celera_gene_source_id;
+ $dep{ACCESSION} = $cg_name;
+ push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
+ }
+
push @xrefs, $xref;
}
--
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