From 20d0e4fdcffb95ef0bc1f12b4bb0101fa73098c6 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 6 Oct 2004 13:13:14 +0000
Subject: [PATCH] made db.pm do the database type stuff
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 119 +++---------------
misc-scripts/xref_mapping/XrefMapper/db.pm | 85 +++++++++++++
2 files changed, 103 insertions(+), 101 deletions(-)
create mode 100644 misc-scripts/xref_mapping/XrefMapper/db.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 5e105cc571..ab80b25e87 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -4,6 +4,12 @@ use strict;
use DBI;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Translation;
+use XrefMapper::db;
+
+use vars '@ISA';
+
+@ISA = qw{ XrefMapper::db };
+
=head1 NAME
@@ -36,30 +42,10 @@ my $xref_password = "ensembl";
-sub new {
- my($class, $species, $host, $port, $dbname, $user, $password ,$dir) = @_;
-
- my $self ={};
- bless $self,$class;
-
- $self->species($species);
- $self->host($host);
- $self->port($port);
- $self->dbname($dbname);
- $self->user($user);
- $self->password($password);
- $self->dir($dir);
-
-
- return $self;
-}
-
-
-
sub dump_seqs{
- my ($self, $slice) = @_;
+ my ($self, $xref) = @_;
$self->dump_ensembl($slice);
- $self->dump_xref();
+ $self->dump_xref($xref);
}
sub run_matching{
@@ -71,13 +57,17 @@ sub store{
}
sub dump_xref{
- my ($self) = @_;
+ my ($self,$xref) = @_;
+
+ if(!defined($xref->species())){
+ $xref->species($self->species);
+ }
#
# the species specified must be in the database and hence have a species_id
#
- my $sql = "select species_id from species where name = '".$self->species."'";
- my $dbi = $self->dbi();
+ my $sql = "select species_id from species where name = '".$xref->species."'";
+ my $dbi = $xref->dbi();
my $sth = $dbi->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
@@ -85,7 +75,7 @@ sub dump_xref{
if (defined @row) {
$species_id = $row[0];
} else {
- print STDERR "Couldn't get ID for species ".$self->species."\n";
+ print STDERR "Couldn't get ID for species ".$xref->species."\n";
print STDERR "It must be one of :-\n";
$sql = "select name from species";
$sth = dbi()->prepare($sql);
@@ -100,8 +90,8 @@ sub dump_xref{
# Dump out the sequences where the species has an id of species_id
# and the sequence type is 'dna'
#
- $self->xref_dna_file($self->dir."/".$self->species."_xref_dna.fasta");
- open(XDNA,">".$self->dir."/".$self->species."_xref_dna.fasta") || die "Could not open xref_dna.fasta";
+ $self->xref_dna_file($self->dir."/".$xref->species."_xref_dna.fasta");
+ open(XDNA,">".$self->dir."/".$xref->species."_xref_dna.fasta") || die "Could not open xref_dna.fasta";
my $sql = "select p.xref_id, p.sequence from primary_xref p, xref x ";
$sql .= "where p.xref_id = x.xref_id and ";
$sql .= " p.sequence_type ='dna' and ";
@@ -209,19 +199,6 @@ FIN:
-sub dbi {
-
- my $self = shift;
-
- my $dbi = DBI->connect("dbi:mysql:host=$xref_host;port=$xref_port;database=$xref_database",
- "$xref_user",
- "$xref_password",
- {'RaiseError' => 1}) || die "Can't connect to database";
-
-
- return $dbi;
-}
-
###
# Getter/Setter methods
###
@@ -268,64 +245,4 @@ sub ensembl_dna_file{
# return \%type;
#}
-sub species {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_species} = $arg );
- return $self->{_species};
-}
-
-sub host {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_host} = $arg );
- return $self->{_host};
-}
-
-
-sub port {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_port} = $arg );
- return $self->{_port};
-}
-
-sub dbname {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_dbname} = $arg );
- return $self->{_dbname};
-}
-
-sub user {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_user} = $arg );
- return $self->{_user};
-}
-
-sub password {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_password} = $arg );
- return $self->{_password};
-}
-
-sub dir {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_dir} = $arg );
- return $self->{_dir};
-}
-
-
-
-
1;
diff --git a/misc-scripts/xref_mapping/XrefMapper/db.pm b/misc-scripts/xref_mapping/XrefMapper/db.pm
new file mode 100644
index 0000000000..5b8f23af91
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/db.pm
@@ -0,0 +1,85 @@
+package XrefMapper::db;
+
+
+sub new {
+ my($class) = @_;
+
+ my $self ={};
+ bless $self,$class;
+
+ print "creating new *$class*\n";
+ return $self;
+}
+
+
+sub species {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_species} = $arg );
+ return $self->{_species};
+}
+
+sub host {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_host} = $arg );
+ return $self->{_host};
+}
+
+
+sub port {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_port} = $arg );
+ return $self->{_port};
+}
+
+sub dbname {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_dbname} = $arg );
+ return $self->{_dbname};
+}
+
+sub user {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_user} = $arg );
+ return $self->{_user};
+}
+
+sub password {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_password} = $arg );
+ return $self->{_password};
+}
+
+sub dir {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_dir} = $arg );
+ return $self->{_dir};
+}
+
+sub dbi {
+
+ my $self = shift;
+
+ my $dbi = DBI->connect("dbi:mysql:host=".$self->host().";port=".$self->port().";database="$self->database(),
+ $self->user,
+ $self->password,
+ {'RaiseError' => 1}) || die "Can't connect to database";
+
+
+ return $dbi;
+}
+
+1;
--
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