diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 3caafac040e9095bdf289ea917c3e70083403c8f..77b4559b2c927b32d3a5689e201b9aac8fc72d4d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -50,8 +50,8 @@ my %source_to_external_db;
my %xrefs_written;
my %object_xrefs_written;
-my $core_dbi;
-my $xref_dbi;
+#my $core_dbi;
+#my $xref_dbi;
=head2 dump_seqs
@@ -73,8 +73,8 @@ sub dump_seqs{
my ($self, $location) = @_;
# initialise DB connections
- $core_dbi = $self->dbi();
- $xref_dbi = $self->xref()->dbi();
+# $core_dbi = $self->dbc;
+# $xref_dbi = $self->xref()->dbc;
$self->dump_xref();
$self->dump_ensembl($location);
@@ -133,10 +133,10 @@ sub build_list_and_map {
=cut
sub get_species_id_from_species_name{
- my ($xref,$species) = @_;
+ my ($self,$species) = @_;
my $sql = "select species_id from species where name = '".$species."'";
- my $sth = $xref_dbi->prepare($sql);
+ my $sth = $self->dbc->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
my $species_id;
@@ -146,7 +146,7 @@ sub get_species_id_from_species_name{
print STDERR "Couldn't get ID for species ".$species."\n";
print STDERR "It must be one of :-\n";
$sql = "select name from species";
- $sth = $xref_dbi->prepare($sql);
+ $sth = $self->dbc->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
print STDERR $row[0]."\n";
@@ -196,11 +196,11 @@ sub get_set_lists{
=cut
sub get_source_id_from_source_name{
- my ($xref, $source) = @_;
+ my ($self, $source) = @_;
my $source_id;
my $sql = "select source_id from source where name = '".$source."'";
- my $sth = $xref_dbi->prepare($sql);
+ my $sth = $self->dbc->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
if (defined $row[0] and $row[0] ne '') {
@@ -210,7 +210,7 @@ sub get_source_id_from_source_name{
print STDERR "Couldn't get ID for source ".$source."\n";
print STDERR "It must be one of :-\n";
$sql = "select name from source";
- $sth = $xref_dbi->prepare($sql);
+ $sth = $self->dbc->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
print STDERR $row[0]."\n";
@@ -373,7 +373,7 @@ sub dump_subset{
$sql .= " LIMIT ".$self->maxdump()." ";
}
- my $sth = $xref->dbi()->prepare($sql);
+ my $sth = $xref->dbc->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
@@ -418,13 +418,7 @@ sub dump_ensembl{
sub fetch_and_dump_seq{
my ($self, $location) = @_;
- my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-species => $self->species(),
- -dbname => $self->dbname(),
- -host => $self->host(),
- -port => $self->port(),
- -pass => $self->password(),
- -user => $self->user(),
- -group => 'core');
+ my $db = $self;
#
# store ensembl dna file name and open it
@@ -776,12 +770,12 @@ sub parse_mappings {
my $dir = $self->dir();
- #create new connections incase old ones have died.
- $core_dbi = $self->dbi();
- $xref_dbi = $self->xref()->dbi();
+ # incase timed out.
+ $self->dbc->connect();
+ $self->xref->dbc->connect();
# get current max object_xref_id
- my $row = @{$core_dbi->selectall_arrayref("SELECT MAX(object_xref_id) FROM object_xref")}[0];
+ my $row = @{$self->dbc->db_handle->selectall_arrayref("SELECT MAX(object_xref_id) FROM object_xref")}[0];
my $max_object_xref_id = @{$row}[0];
if (!defined $max_object_xref_id) {
print "Can't get highest existing object_xref_id, using 1\n";
@@ -792,7 +786,7 @@ sub parse_mappings {
my $object_xref_id_offset = $max_object_xref_id + 1;
my $object_xref_id = $object_xref_id_offset;
- $row = @{$self->dbi->selectall_arrayref("SELECT MAX(xref_id) FROM xref")}[0];
+ $row = @{$self->dbc->db_handle->selectall_arrayref("SELECT MAX(xref_id) FROM xref")}[0];
my $max_xref_id = @$row[0];
if (!defined $max_xref_id) {
print "Can't get highest existing xref_id, using 1\n";
@@ -924,7 +918,7 @@ sub dump_orphan_xrefs() {
# need a double left-join
my $sql = "SELECT x.xref_id, x.accession, x.version, x.label, x.description, x.source_id, x.species_id FROM xref x LEFT JOIN primary_xref px ON px.xref_id=x.xref_id LEFT JOIN dependent_xref dx ON dx.dependent_xref_id=x.xref_id WHERE px.xref_id IS NULL AND dx.dependent_xref_id IS NULL";
- my $sth = $xref_dbi->prepare($sql);
+ my $sth = $self->xref->dbc->prepare($sql);
$sth->execute();
my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id);
@@ -967,7 +961,7 @@ sub dump_direct_xrefs {
# Will need to look up translation stable ID from transcript stable ID, build hash table
print "Building transcript stable ID -> translation stable ID lookup table\n";
my %transcript_stable_id_to_translation_stable_id;
- my $trans_sth = $core_dbi->prepare("SELECT tss.stable_id as transcript, tls.stable_id AS translation FROM translation tl, translation_stable_id tls, transcript_stable_id tss WHERE tss.transcript_id=tl.transcript_id AND tl.translation_id=tls.translation_id");
+ my $trans_sth = $self->dbc->prepare("SELECT tss.stable_id as transcript, tls.stable_id AS translation FROM translation tl, translation_stable_id tls, transcript_stable_id tss WHERE tss.transcript_id=tl.transcript_id AND tl.translation_id=tls.translation_id");
$trans_sth->execute();
my ($transcript_stable_id, $translation_stable_id);
$trans_sth->bind_columns(\$transcript_stable_id, \$translation_stable_id);
@@ -981,7 +975,7 @@ sub dump_direct_xrefs {
# SQL / statement handle for getting all direct xrefs
my $xref_sql = "SELECT dx.general_xref_id, dx.ensembl_stable_id, dx.type, dx.linkage_xref, x.accession, x.version, x.label, x.description, x.source_id, x.species_id FROM direct_xref dx, xref x WHERE dx.general_xref_id=x.xref_id";
- my $xref_sth = $xref_dbi->prepare($xref_sql);
+ my $xref_sth = $self->xref->dbc->prepare($xref_sql);
$xref_sth->execute();
@@ -1071,7 +1065,7 @@ sub dump_interpro {
open (INTERPRO, ">" . $self->dir() . "/interpro.txt");
- my $sth = $xref_dbi->prepare("SELECT * FROM interpro");
+ my $sth = $self->xref->dbc->prepare("SELECT * FROM interpro");
$sth->execute();
my ($interpro, $pfam);
@@ -1096,7 +1090,7 @@ sub build_stable_id_to_internal_id_hash {
print "Caching stable ID -> internal ID links for ${type}s\n";
my $core_sql = "SELECT ${type}_id, stable_id FROM ${type}_stable_id" ;
- my $sth = $core_dbi->prepare($core_sql);
+ my $sth = $self->dbc->prepare($core_sql);
$sth->execute();
my ($internal_id, $stable_id);
$sth->bind_columns(\$internal_id, \$stable_id);
@@ -1158,7 +1152,7 @@ sub get_analysis_id {
my $logic_name = $typeToLogicName{lc($ensembl_type)};
- my $sth = $core_dbi->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
+ my $sth = $self->dbc->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
$sth->execute();
my $analysis_id;
@@ -1171,7 +1165,7 @@ sub get_analysis_id {
} else {
print "No analysis with logic_name $logic_name found, creating ...\n";
- $sth = $core_dbi->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
+ $sth = $self->dbc->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
# TODO - other fields in analysis table
$sth->execute();
$analysis_id = $sth->{'mysql_insertid'};
@@ -1232,7 +1226,7 @@ sub dump_core_xrefs {
my $sql = "SELECT * FROM xref WHERE xref_id $id_str";
- my $xref_sth = $xref_dbi->prepare($sql);
+ my $xref_sth = $self->xref->dbc->prepare($sql);
$xref_sth->execute();
my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id, $master_xref_id, $linkage_annotation);
@@ -1262,7 +1256,7 @@ sub dump_core_xrefs {
$sql = "SELECT DISTINCT(x.xref_id), dx.master_xref_id, x.accession, x.label, x.description, x.source_id, x.version, dx.linkage_annotation 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);
+ my $dep_sth = $self->xref->dbc->prepare($sql);
$dep_sth->execute();
$dep_sth->bind_columns(\$xref_id, \$master_xref_id, \$accession, \$label, \$description, \$source_id, \$version, \$linkage_annotation);
@@ -1312,7 +1306,7 @@ sub dump_core_xrefs {
# Now get the synonyms for each of these xrefs and write them to the external_synonym table
$sql = "SELECT DISTINCT xref_id, synonym FROM synonym WHERE xref_id $id_str";
- my $syn_sth = $xref_dbi->prepare($sql);
+ my $syn_sth = $self->xref->dbc->prepare($sql);
$syn_sth->execute();
$syn_sth->bind_columns(\$xref_id, \$accession);
@@ -1336,7 +1330,7 @@ sub dump_core_xrefs {
# calculate display_xref_ids for transcripts and genes
my $transcript_display_xrefs = $self->build_transcript_display_xrefs($xref_id_offset);
- build_genes_to_transcripts();
+ $self->build_genes_to_transcripts();
$self->build_gene_display_xrefs($transcript_display_xrefs);
@@ -1397,7 +1391,7 @@ sub build_transcript_display_xrefs {
# note %xref_to_source is global
print "Building xref->source mapping table\n";
my $sql = "SELECT x.xref_id, s.name FROM source s, xref x WHERE x.source_id=s.source_id";
- my $sth = $xref_dbi->prepare($sql);
+ my $sth = $self->xref->dbc->prepare($sql);
$sth->execute();
my ($xref_id, $source_name);
@@ -1412,7 +1406,7 @@ sub build_transcript_display_xrefs {
# Cache the list of translation->transcript mappings & vice versa
# Nte variables are global
print "Building translation to transcript mappings\n";
- my $sth = $core_dbi->prepare("SELECT translation_id, transcript_id FROM translation");
+ my $sth = $self->dbc->prepare("SELECT translation_id, transcript_id FROM translation");
$sth->execute();
my ($translation_id, $transcript_id);
@@ -1577,13 +1571,15 @@ sub build_gene_display_xrefs {
my $dir = $self->dir();
- my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-species => $self->species(),
- -dbname => $self->dbname(),
- -host => $self->host(),
- -port => $self->port(),
- -pass => $self->password(),
- -user => $self->user(),
- -group => 'core');
+# my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-species => $self->species(),
+# -dbname => $self->dbc->dbname(),
+# -host => $self->host(),
+# -port => $self->port(),
+# -pass => $self->password(),
+# -user => $self->user(),
+# -group => 'core');
+ my $db = $self;
+
my $ta = $db->get_TranscriptAdaptor();
print "Assigning display_xrefs to genes\n";
@@ -1682,7 +1678,7 @@ sub build_genes_to_transcripts {
print "Getting transcripts for all genes\n";
my $sql = "SELECT gene_id, transcript_id FROM transcript";
- my $sth = $core_dbi->prepare($sql);
+ my $sth = $self->dbc->prepare($sql);
$sth->execute();
my ($gene_id, $transcript_id);
@@ -1745,7 +1741,7 @@ sub map_source_to_external_db {
my %source_to_external_db;
# get all sources
- my $sth = $self->xref->dbi()->prepare("SELECT source_id, name FROM source");
+ my $sth = $self->xref->dbc->prepare("SELECT source_id, name FROM source");
$sth->execute();
my ($source_id, $source_name);
$sth->bind_columns(\$source_id, \$source_name);
@@ -1754,7 +1750,7 @@ sub map_source_to_external_db {
# find appropriate external_db_id for each one
my $sql = "SELECT external_db_id FROM external_db WHERE db_name=?";
- my $core_sth = $core_dbi->prepare($sql);
+ my $core_sth = $self->dbc->prepare($sql);
$core_sth->execute($source_name);
my @row = $core_sth->fetchrow_array();
@@ -1792,14 +1788,14 @@ sub do_upload {
if ($deleteexisting) {
- $sth = $core_dbi->prepare("DELETE FROM $table");
+ $sth = $self->dbc->prepare("DELETE FROM $table");
print "Deleting existing data in $table\n";
$sth->execute();
}
# don't seem to be able to use prepared statements here
- $sth = $core_dbi->prepare("LOAD DATA INFILE \'$file\' IGNORE INTO TABLE $table");
+ $sth = $self->dbc->prepare("LOAD DATA INFILE \'$file\' IGNORE INTO TABLE $table");
print "Uploading data in $file to $table\n";
$sth->execute();
@@ -1813,17 +1809,17 @@ sub do_upload {
if ($deleteexisting) {
- $sth = $core_dbi->prepare("UPDATE $table SET display_xref_id=NULL");
+ $sth = $self->dbc->prepare("UPDATE $table SET display_xref_id=NULL");
print "Setting all existing display_xref_id in $table to null\n";
$sth->execute();
}
print "Setting $table display_xrefs from $file\n";
- my $str = "mysql -u " .$self->user() ." -p" . $self->password() . " -h " . $self->host() ." -P " . $self->port() . " " .$self->dbname() . " < $file";
+ my $str = "mysql -u " .$self->user() ." -p" . $self->password() . " -h " . $self->host() ." -P " . $self->port() . " " .$self->dbc->dbname() . " < $file";
system $str;
- #$sth = $core_dbi->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
+ #$sth = $self->dbc->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
#open(DX_TXT, $file);
#while (<DX_TXT>) {
# my ($xref_id, $object_id) = split;
@@ -1871,7 +1867,7 @@ sub build_gene_descriptions {
print "Getting & filtering xref descriptions\n";
# Note %xref_descriptions & %xref_accessions are global
- my $sth = $self->xref->dbi()->prepare("SELECT xref_id, accession, description FROM xref");
+ my $sth = $self->xref->dbc->prepare("SELECT xref_id, accession, description FROM xref");
$sth->execute();
my ($xref_id, $accession, $description);
$sth->bind_columns(\$xref_id, \$accession, \$description);
@@ -2049,14 +2045,16 @@ sub compare_xref_descriptions {
# load external_db (if it's empty) from ../external_db/external_dbs.txt
sub upload_external_db {
+ my ($self) = @_;
- my $row = @{$core_dbi->selectall_arrayref("SELECT COUNT(*) FROM external_db")}[0];
+ $self->dbc->connect();
+ my $row = @{$self->dbc->db_handle->selectall_arrayref("SELECT COUNT(*) FROM external_db")}[0];
my $count = @{$row}[0];
if ($count == 0) {
my $edb = cwd() . "/../external_db/external_dbs.txt";
print "external_db table is empty, uploading from $edb\n";
- my $edb_sth = $core_dbi->prepare("LOAD DATA INFILE \'$edb\' INTO TABLE external_db");
+ my $edb_sth = $self->dbc->prepare("LOAD DATA INFILE \'$edb\' INTO TABLE external_db");
$edb_sth->execute();
} else {
print "external_db table already has $count rows, will not change it\n";
diff --git a/misc-scripts/xref_mapping/XrefMapper/db.pm b/misc-scripts/xref_mapping/XrefMapper/db.pm
index a3acb797ab9e6dc81992107147db889e188b1882..19f00057d63c0e594a96f18cb68e773852b013be 100644
--- a/misc-scripts/xref_mapping/XrefMapper/db.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/db.pm
@@ -1,166 +1,13 @@
package XrefMapper::db;
+use vars '@ISA';
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Utils::ConfigRegistry;
-=head2 new
- Example : $db = new XrefMapper::db();
- Description: Creates new db object.
- Returntype : XrefMapper::db;
- Exceptions : none
- Caller : general
-
-=cut
-
-
-sub new {
- my($class) = @_;
-
- my $self ={};
- bless $self,$class;
-
- return $self;
-}
-
-
-=head2 species
-
- Arg [1] : (optional) string $arg
- The new value of the species used by this connection.
- Example : $host = $db->species()
- Description: Getter/Setter for the species of to use for
- this connection. There is currently no point in setting
- this value after the connection has already been established
- by the constructor.
- Returntype : string
- Exceptions : none
- Caller : new
-
-=cut
-
-sub species {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_species} = $arg );
- return $self->{_species};
-}
-
-=head2 host
-
- Arg [1] : (optional) string $arg
- The new value of the host used by this connection.
- Example : $host = $db->host()
- Description: Getter/Setter for the domain name of the database host use by
- this connection. There is currently no point in setting
- this value after the connection has already been established
- by the constructor.
- Returntype : string
- Exceptions : none
- Caller : new
-
-=cut
-
-sub host {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_host} = $arg );
- return $self->{_host};
-}
-
-=head2 port
-
- Arg [1] : (optional) int $arg
- the TCP or UDP port to use to connect to the database
- Example : $port = $db->port();
- Description: Getter / Setter for the port this connection uses to communicate
- to the database daemon. There currently is no point in
- setting this value after the connection has already been
- established by the constructor.
- Returntype : string
- Exceptions : none
- Caller : new
-
-=cut
-
-
-sub port {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_port} = $arg );
- return $self->{_port};
-}
-
-=head2 dbname
-
- Arg [1] : (optional) string $arg
- The new value of the database name used by this connection.
- Example : $dbname = $db->dbname()
- Description: Getter/Setter for the name of the database used by this
- connection. There is currently no point in setting this value
- after the connection has already been established by the
- constructor.
- Returntype : string
- Exceptions : none
- Caller : new
-
-=cut
-
-sub dbname {
- my ($self, $arg) = @_;
+@ISA = qw{Bio::EnsEMBL::DBSQL::DBAdaptor};
- (defined $arg) &&
- ($self->{_dbname} = $arg );
- return $self->{_dbname};
-}
-
-=head2 user
-
- Arg [1] : (optional) string $arg
- The new value of the username used by this connection.
- Example : $user = $db->user()
- Description: Getter/Setter for the username used by this
- connection. There is currently no point in setting this value
- after the connection has already been established by the
- constructor.
- Returntype : string
- Exceptions : none
- Caller : new
-
-=cut
-
-sub user {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_user} = $arg );
- return $self->{_user};
-}
-
-=head2 password
-
- Arg [1] : (optional) string $arg
- The new value of the password used by this connection.
- Example : $pass = $db->password()
- Description: Getter/Setter for the password of to use for
- this connection. There is currently no point in setting
- this value after the connection has already been established
- by the constructor.
- Returntype : string
- Exceptions : none
- Caller : new
-
-=cut
-
-
-sub password {
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_password} = $arg );
- return $self->{_password};
-}
=head2 dir
@@ -231,27 +78,5 @@ sub process_dir {
return $dir;
}
-=head2 dbi
-
- Example : $dbi = $db->dbi()
- Description: creates a new dbi connection
- Returntype : DBI
- Exceptions : will die if database is not connected to properly.
- Caller : general
-
-=cut
-
-sub dbi {
-
- my $self = shift;
-
- 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";
-
-
- return $dbi;
-}
1;
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index 33e4c14819a0e4cf55bdc623341bf547cd75f06a..b4e334949d7cc797e561264e3c526d6bd011ff4d 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -48,6 +48,9 @@ my $xref=undef;
my $species=undef;
my $type;
+my %xref_hash=();
+my %species_hash=();
+
while( my $line = <FILE> ) {
chomp($line);
@@ -58,80 +61,136 @@ while( my $line = <FILE> ) {
my ($key, $value) = split("=",$line);
if($key eq "species"){
$type = "species";
- if(defined($species)){
- push @all_species, $species;
- $species = undef;
- }
-
- if ($value !~ /_/) {
- print STDERR "\'$value\' is not a recognised species - please use full species name (e.g. homo_sapiens) in $file\n";
- exit(1);
- }
-
- eval "require XrefMapper::$value";
- my $module;
- if($@) {
- warn("Did not find a specific mapping module XrefMapper::$value - using XrefMapper::BasicMapper instead\n");
- require XrefMapper::BasicMapper;
- $module = "BasicMapper";
- } else{
- $module = $value;
- }
-
- no strict 'refs';
- $species = "XrefMapper::$module"->new();
- $species->species($value);
-
- if(defined($dumpcheck)){
- $species->dumpcheck("yes");
- }
- if(defined($maxdump)){
- $species->maxdump($maxdump);
- }
- if(defined($use_existing_mappings)){
- $species->use_existing_mappings("yes");
- }
-
+ $species_hash{'species'} = $value;
}
elsif($key eq "xref"){
$type = "xref";
- $xref = new XrefMapper::db();
}
elsif($type eq "species"){ # processing species data
- $species->$key($value);
+ $species_hash{lc($key)} = $value;
}
elsif($type eq "xref"){ # processing xref data
- $xref->$key($value);
+ $xref_hash{lc($key)} = $value;
+ }
+}
+
+if(defined($xref_hash{host})){
+ my ($host, $user, $dbname, $pass, $port);
+ $host = $xref_hash{'host'};
+ $user = $xref_hash{'user'};
+ $dbname = $xref_hash{'dbname'};
+ if(defined($xref_hash{'pass'})){
+ $pass = $xref_hash{'pass'};
+ }
+ else{
+ $pass = '';
+ }
+ if(defined($xref_hash{'port'})){
+ $port = $xref_hash{'port'};
+ }
+ else{
+ $port = 3306;
}
+
+ $xref = new XrefMapper::db(-host => $host,
+ -port => $port,
+ -user => $user,
+ -pass => $pass,
+ -group => 'core',
+ -dbname => $dbname);
+
+ if(defined($xref_hash{'dir'})){
+ $xref->dir($xref_hash{'dir'});
+ }
+
}
-if(defined($species)){
- push @all_species, $species;
+else{
+ die "No host name given for xref\n";
}
-my $i = 1;
+if(defined($species_hash{'species'})){
+ my $value = $species_hash{'species'};
+ if ($value !~ /_/) {
+ print STDERR "\'$value\' is not a recognised species - please use full species name (e.g. homo_sapiens) in $file\n";
+ exit(1);
+ }
+
+ eval "require XrefMapper::$value";
+ my $module;
+ if($@) {
+ warn("Did not find a specific mapping module XrefMapper::$value - using XrefMapper::BasicMapper instead\n");
+ require XrefMapper::BasicMapper;
+ $module = "BasicMapper";
+ } else{
+ $module = $value;
+ }
+
+ no strict 'refs';
+ my ($host, $port, $user, $dbname, $pass);
+ $host = $species_hash{'host'};
+ $user = $species_hash{'user'};
+ $dbname = $species_hash{'dbname'};
+ if(defined($species_hash{'pass'})){
+ $pass = $species_hash{'pass'};
+ }
+ else{
+ $pass = '';
+ }
+ if(defined($species_hash{'port'})){
+ $port = $species_hash{'port'};
+ }
+ else{
+ $port = '';
+ }
+
+ $species = "XrefMapper::$module"->new(-host => $host,
+ -port => $port,
+ -user => $user,
+ -pass => $pass,
+ -species => $value,
+ -group => 'core',
+ -dbname => $dbname);
+
+ if(defined($species_hash{'dir'})){
+ $species->dir($species_hash{'dir'});
+ }
+
+ $species->species($value);
+
+ if(defined($dumpcheck)){
+ $species->dumpcheck("yes");
+ }
+ if(defined($maxdump)){
+ $species->maxdump($maxdump);
+ }
+ if(defined($use_existing_mappings)){
+ $species->use_existing_mappings("yes");
+ }
-for my $species ( @all_species ) {
+
+}
+else{
+ die "No Species given\n";
+}
- $species->xref($xref); # attach xref object to species object
- print "\nDumping xref & Ensembl sequences" . info($i, @all_species) . "\n";
- $species->dump_seqs($location);
+$species->xref($xref); # attach xref object to species object
- print "\nChecking external_db table\n" if ($upload);
- $species->upload_external_db() if ($upload);
+print "\nDumping xref & Ensembl sequences\n";
+$species->dump_seqs($location);
- print "\nRunning mapping" . info($i, @all_species) . "\n";
- $species->build_list_and_map();
+print "\nChecking external_db table\n" if ($upload);
+$species->upload_external_db() if ($upload);
- print "\nParsing mapping output" . info($i, @all_species) . "\n";
- $species->parse_mappings();
+print "\nRunning mapping\n";
+$species->build_list_and_map();
- print "\nUploading xrefs" . info($i, @all_species) . "\n" if ($upload);
- $species->do_upload($deleteexisting) if ($upload);
+print "\nParsing mapping output\n";
+$species->parse_mappings();
- $i++;
+print "\nUploading xrefs\n" if ($upload);
+$species->do_upload($deleteexisting) if ($upload);
-}
print STDERR "*** All finished ***\n";