From e9edededd560f59ad6e388447443d77a8eb2f20a Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 14 Jul 2011 14:46:22 +0000
Subject: [PATCH] set type to DIRECT for the direct xrefs
---
.../xref_mapping/XrefParser/FlybaseParser.pm | 18 +++++++-----------
1 file changed, 7 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm b/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
index 1c8872b5b7..afb6033b2a 100644
--- a/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
@@ -122,8 +122,7 @@ sub get_source_id_for_source_name {
}
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -132,9 +131,6 @@ sub run {
my $data_file = @{$files}[0];
-# my $self = shift;
-# my ( $source_id, $species_id, $data_file, $release_file ) = @_;
-
# Fetch hashes of already stored Uniprot and Interpro accessions.
my %pre_xref_ids = (
'Uniprot' => $self->get_valid_codes( 'uniprot', $species_id ),
@@ -255,11 +251,11 @@ sub run {
if ( $dbxref_name eq 'bdgpinsituexpr' ) {
$xref_id =
$self->add_xref( $id, undef, $accession, '',
- $source_id, $species_id );
+ $source_id, $species_id, 'DIRECT' );
} else {
$xref_id =
$self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id );
+ $source_id, $species_id, 'DIRECT' );
}
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -286,7 +282,7 @@ sub run {
} else {
$xref_id =
$self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id );
+ $source_id, $species_id ,'DIRECT');
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -311,7 +307,7 @@ sub run {
} else {
$xref_id =
$self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id );
+ $source_id, $species_id, 'DIRECT' );
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -337,7 +333,7 @@ sub run {
} else {
$xref_id =
$self->add_xref( $id, undef, $accession, '', $source_id,
- $species_id );
+ $species_id, 'DIRECT' );
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -360,7 +356,7 @@ sub run {
} else {
$xref_id =
$self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id );
+ $source_id, $species_id, 'DIRECT' );
$xref_ids{$source_name}{$accession} = $xref_id;
}
--
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