From 853c2dd9192f47e68c3c8cb2542ac28955a16029 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 6 Oct 2004 14:16:37 +0000
Subject: [PATCH] small fixes for new input format
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 6 +++---
misc-scripts/xref_mapping/XrefMapper/db.pm | 2 +-
misc-scripts/xref_mapping/xref_mapper.input | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index ab80b25e87..b2313c8b4c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -44,7 +44,7 @@ my $xref_password = "ensembl";
sub dump_seqs{
my ($self, $xref) = @_;
- $self->dump_ensembl($slice);
+ $self->dump_ensembl();
$self->dump_xref($xref);
}
@@ -96,7 +96,7 @@ sub dump_xref{
$sql .= "where p.xref_id = x.xref_id and ";
$sql .= " p.sequence_type ='dna' and ";
$sql .= " x.species_id = ".$species_id." ";
- $sth = dbi()->prepare($sql);
+ $sth = $xref->dbi()->prepare($sql);
$sth->execute();
my $i = 0;
while(my @row = $sth->fetchrow_array()){
@@ -120,7 +120,7 @@ ENDDNA:
$sql .= "where p.xref_id = x.xref_id and ";
$sql .= " p.sequence_type ='peptide' and ";
$sql .= " x.species_id = ".$species_id." ";
- $sth = dbi()->prepare($sql);
+ $sth = $xref->dbi()->prepare($sql);
$sth->execute();
$i = 0;
while(my @row = $sth->fetchrow_array()){
diff --git a/misc-scripts/xref_mapping/XrefMapper/db.pm b/misc-scripts/xref_mapping/XrefMapper/db.pm
index 5b8f23af91..047a1bbdcf 100644
--- a/misc-scripts/xref_mapping/XrefMapper/db.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/db.pm
@@ -73,7 +73,7 @@ sub dbi {
my $self = shift;
- my $dbi = DBI->connect("dbi:mysql:host=".$self->host().";port=".$self->port().";database="$self->database(),
+ my $dbi = DBI->connect("dbi:mysql:host=".$self->host().";port=".$self->port().";database=".$self->dbname(),
$self->user,
$self->password,
{'RaiseError' => 1}) || die "Can't connect to database";
diff --git a/misc-scripts/xref_mapping/xref_mapper.input b/misc-scripts/xref_mapping/xref_mapper.input
index 7caffcd388..ce7a273fa4 100644
--- a/misc-scripts/xref_mapping/xref_mapper.input
+++ b/misc-scripts/xref_mapping/xref_mapper.input
@@ -9,7 +9,7 @@ dir=./xref
species=homo_sapiens
host=ecs2
port=3365
-dbname=homo_sapiens_core_24_34e
+dbname=homo_sapiens_core_25_34e
user=ensro
password=
dir=./test
--
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