From f693f3b3978d46aa1df3258a18f85a3f5a820c1c Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 13 Oct 2004 15:00:44 +0000
Subject: [PATCH] Fixed dependent xref dumping SQL.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 34 +++++++++++--------
1 file changed, 19 insertions(+), 15 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 5c5b061d09..7a5d0c2306 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -2,10 +2,11 @@ package XrefMapper::BasicMapper;
use strict;
use DBI;
+use File::Basename;
use IPC::Open3;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Translation;
-use XrefMapper::db;
+use XrefMapper::db;
use vars '@ISA';
@@ -664,12 +665,7 @@ sub submit_depend_job {
sub store {
- my ($self, $xref, $target_file_name) = @_;
-
- my $type = get_ensembl_object_type($target_file_name);
-
- # get or create the appropriate analysis ID
- my $analysis_id = $self->get_analysis_id($type);
+ my ($self, $xref) = @_;
# get current max object_xref_id
my $max_object_xref_id = 0;
@@ -701,10 +697,18 @@ sub store {
my $dir = $self->dir();
foreach my $file (glob("$dir/*.map")) {
- print "Parsing results from $file \n";
+ print "Parsing results from " . basename($file) . "\n";
open(FILE, $file);
$total_files++;
+ # files are named Method_(dna|prot)_N.map
+ my $type = get_ensembl_object_type($file);
+
+ # get or create the appropriate analysis ID
+ # XXX restore when using writeable database
+ #my $analysis_id = $self->get_analysis_id($type);
+ my $analysis_id = 999;
+
while (<FILE>) {
$total_lines++;
@@ -751,11 +755,13 @@ sub get_ensembl_object_type {
my $filename = shift;
my $type;
- if ($filename =~ /_dna\./i) {
+ $filename = basename($filename);
+
+ if ($filename =~ /_dna_/i) {
$type = "Transcript";
- } elsif ($filename =~ /_protein\./i) {
+ } elsif ($filename =~ /_prot_/i) {
$type = "Translation";
@@ -764,7 +770,6 @@ sub get_ensembl_object_type {
print STDERR "Cannot deduce Ensembl object type from filename $filename\n";
}
-print "###$filename $type\n";
return $type;
}
@@ -812,9 +817,7 @@ sub dump_xrefs {
open (XREF, ">xref.txt");
- # TODO - get this from config
my $xref_dbi = $self->xref()->dbi();
-
my $core_dbi = $self->dbi();
# get current highest internal ID from xref
@@ -869,11 +872,12 @@ sub dump_xrefs {
}
# Now get the dependent xrefs for each of these xrefs and write them as well
- $sql = "SELECT x.accession, x.label, x.description, x.source_id FROM dependent_xref dx, xref x WHERE x.xref_id=dx.master_xref_id AND master_xref_id $id_str";
+ $sql = "SELECT DISTINCT(x.xref_id), x.accession, x.label, x.description, x.source_id FROM dependent_xref dx, xref x WHERE x.xref_id=dx.dependent_xref_id AND master_xref_id $id_str";
+
my $dep_sth = $xref_dbi->prepare($sql);
$dep_sth->execute();
- $dep_sth->bind_columns(\$accession, \$label, \$description, \$source_id);
+ $dep_sth->bind_columns(\$xref_id, \$accession, \$label, \$description, \$source_id);
while (my @row = $dep_sth->fetchrow_array()) {
print XREF "$core_xref_id\t$accession\t$label\t$description\tDEPENDENT\n";
$source_ids{$source_id} = $source_id;
--
GitLab