From bb43f574a511de9c1e5dc47ff58ac99c7b1c1f6f Mon Sep 17 00:00:00 2001
From: Will Spooner <whs@sanger.ac.uk>
Date: Tue, 12 Jun 2007 09:24:17 +0000
Subject: [PATCH] Added evals to retrieval of hard-coded sources (wormbase,
CCDS) so that the script does not crash if these are missing. Also added
count_unmapped_reasons method for validation of the unmapped_reasons table in
the target DB
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 44 ++++++++++++++-----
misc-scripts/xref_mapping/xref_mapper.pl | 6 +++
2 files changed, 40 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index cadfccab1a..b49bca5fd5 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -859,8 +859,8 @@ sub run_mapping {
# delete old output files in target directory if we're going to produce new ones
if (!defined($self->use_existing_mappings())) {
- print "Deleting out, err and map files from output dir\n";
my $dir = $self->core->dir();
+ print "Deleting out, err and map files from output dir: $dir\n";
unlink (<$dir/*.map $dir/*.out $dir/*.err>);
}
$self->remove_all_old_output_files();
@@ -1847,7 +1847,11 @@ XSQL
my %error_count;
my %error_example;
- my $ccds_source = get_source_id_from_source_name($self->xref(), "CCDS");
+ my $ccds_source;
+ eval{ $ccds_source =
+ get_source_id_from_source_name($self->xref(), "CCDS") };
+ if( $@ and $@ !~ /^Please try again/){ die( "==> $@" ) }
+
while ($xref_sth->fetch()) {
my $external_db_id = $source_to_external_db{$source_id};
@@ -1956,11 +1960,23 @@ XSQL
} else {
if(!defined($worm_pep_source_id)){
- $worm_pep_source_id = get_source_id_from_source_name($self->xref(), "wormpep_id");
- $worm_locus_source_id = get_source_id_from_source_name($self->xref(), "wormbase_locus");
- $worm_gene_source_id = get_source_id_from_source_name($self->xref(), "wormbase_gene");
- $worm_transcript_source_id = get_source_id_from_source_name($self->xref(), "wormbase_transcript");
- $go_source_id = get_source_id_from_source_name($self->xref(), "GO" );
+ # Non-standard handling of WormBase stuff
+ eval{ $worm_pep_source_id = get_source_id_from_source_name
+ ($self->xref(), "wormpep_id") };
+ if( $@ and $@ !~ /^Please try again/){ die( "==> $@" ) }
+ eval{ $worm_locus_source_id = get_source_id_from_source_name
+ ($self->xref(), "wormbase_locus") };
+ if( $@ and $@ !~ /^Please try again/){ die( "==> $@" ) }
+ eval{ $worm_gene_source_id = get_source_id_from_source_name
+ ($self->xref(), "wormbase_gene") };
+ if( $@ and $@ !~ /^Please try again/){ die( "==> $@" ) }
+ eval{ $worm_transcript_source_id = get_source_id_from_source_name
+ ($self->xref(), "wormbase_transcript") };
+ if( $@ and $@ !~ /^Please try again/){ die( "==> $@" ) }
+ eval{ $go_source_id = get_source_id_from_source_name
+ ($self->xref(), "GO" ) };
+ if( $@ and $@ !~ /^Please try again/){ die( "==> $@" ) }
+ $worm_pep_source_id ||= 0;
}
# deal with UTR transcripts in Elegans and potentially others
# Need to link xrefs that are listed as linking to e.g. ZK829.4
@@ -2183,9 +2199,8 @@ sub remove_all_old_output_files{
my $dir = $self->core->dir();
- print "Deleting txt and sql files from output dir\n";
+ print "Deleting txt and sql files from output dir: $dir\n";
unlink(<$dir/*.txt $dir/*.sql>);
-
}
sub dump_core_xrefs {
@@ -4140,7 +4155,16 @@ PSQL
}
-
+sub count_unmapped_reasons{
+ # Returns the number of entries in the unmapped_reason table
+ my $self = shift;
+ my $sth = $self->core->dbc->prepare
+ ("select count(*) from unmapped_reason" );
+ $sth->execute();
+ my $count = ($sth->fetchrow_array)[0];
+ $sth->finish;
+ return $count;
+}
sub unmapped_data_for_prioritys{
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index d2d0c3b117..2c863d6d33 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -361,6 +361,12 @@ $mapper->find_priority_sources();
print "\nParsing mapping output\n";
+unless( $notriage and ! $mapper->count_unmapped_reasons ){
+ die( "The unmapped_reasons table in the target database is empty. ",
+ "Either run this script using the -notriage flag, ",
+ "or populate the table using e.g. ",
+ "ensembl/misc-scripts/unmapped_reason/update_unmapped_reasons.pl\n" );
+}
$mapper->parse_mappings($notriage);
--
GitLab