diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 77b4559b2c927b32d3a5689e201b9aac8fc72d4d..2b26d02f051fb9146c0270c094783042ad15857c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -9,10 +9,6 @@ use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Translation;
use XrefMapper::db;
-use vars '@ISA';
-
-@ISA = qw{ XrefMapper::db };
-
=head1 NAME
@@ -50,8 +46,24 @@ my %source_to_external_db;
my %xrefs_written;
my %object_xrefs_written;
-#my $core_dbi;
-#my $xref_dbi;
+=head2 new
+
+ Description: Constructor for BasicMapper.
+ Returntype : BasicMapper
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub new{
+ my($class, @args) = @_;
+
+ my $self ={};
+ bless $self,$class;
+
+ return $self;
+}
+
=head2 dump_seqs
@@ -72,10 +84,6 @@ sub dump_seqs{
my ($self, $location) = @_;
- # initialise DB connections
-# $core_dbi = $self->dbc;
-# $xref_dbi = $self->xref()->dbc;
-
$self->dump_xref();
$self->dump_ensembl($location);
@@ -105,12 +113,12 @@ sub build_list_and_map {
my @dna=();
push @dna, $method;
push @dna, $self->xref->dir."/xref_".$i."_dna.fasta";
- push @dna, $self->ensembl_dna_file();
+ push @dna, $self->core->dna_file();
push @list, \@dna;
my @pep=();
push @pep, $method;
push @pep, $self->xref->dir."/xref_".$i."_peptide.fasta";
- push @pep, $self->ensembl_protein_file();
+ push @pep, $self->core->protein_file();
push @list, \@pep;
$i++;
}
@@ -135,12 +143,13 @@ sub build_list_and_map {
sub get_species_id_from_species_name{
my ($self,$species) = @_;
+
my $sql = "select species_id from species where name = '".$species."'";
my $sth = $self->dbc->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
my $species_id;
- if (defined @row) {
+ if (@row) {
$species_id = $row[0];
} else {
print STDERR "Couldn't get ID for species ".$species."\n";
@@ -173,12 +182,6 @@ sub get_species_id_from_species_name{
sub get_set_lists{
my ($self) = @_;
- # return [["ExonerateGappedBest1", ["homo_sapiens","Uniprot/SWISSPROT"]]];
-
-# return [["method1",["homo_sapiens","RefSeq"],["homo_sapiens","UniProtSwissProt"]],
-# ["method2",[$self->species,"*"]],
-# ["method3",["*","*"]]];
-
return [["ExonerateGappedBest1", ["*","*"]]];
}
@@ -205,7 +208,6 @@ sub get_source_id_from_source_name{
my @row = $sth->fetchrow_array();
if (defined $row[0] and $row[0] ne '') {
$source_id = $row[0];
-# print $source."\t*".$row[0]."*\n";
} else {
print STDERR "Couldn't get ID for source ".$source."\n";
print STDERR "It must be one of :-\n";
@@ -275,14 +277,12 @@ sub dump_xref{
$i=0;
foreach my $list (@lists){
-# print "method->".@$list[0]."\n";
$method[$i] = shift @$list;
my $j = 0;
my @source_id=();
my @species_id=();
foreach my $element (@$list){
while(my $species = shift(@$element)){
- # print $j.")\t".$species."\n";
if($species ne "*"){
$species_id[$j] = get_species_id_from_species_name($xref,$species);
}
@@ -296,8 +296,6 @@ sub dump_xref{
else{
$source_id[$j] = -1;
}
-# print $j."\t".$source. "\t".$source_id[$j] ."\n";
-# print $j."\t".$species."\t".$species_id[$j]."\n";
$j++;
}
}
@@ -418,30 +416,32 @@ sub dump_ensembl{
sub fetch_and_dump_seq{
my ($self, $location) = @_;
- my $db = $self;
+ my $ensembl = $self->core;
+ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-dbconn => $ensembl->dbc);
#
# store ensembl dna file name and open it
#
-
- # if no directory set then dump in the current directory.
- if(!defined($self->dir())){
- $self->dir(".");
+ if(!defined($ensembl->dir())){
+ $ensembl->dir(".");
}
- $self->ensembl_dna_file($self->dir."/".$self->species."_dna.fasta");
+ $ensembl->dna_file($ensembl->dir."/".$ensembl->species."_dna.fasta");
+
+
#
# store ensembl protein file name and open it
#
- $self->ensembl_protein_file($self->dir."/".$self->species."_protein.fasta");
+ $ensembl->protein_file($ensembl->dir."/".$ensembl->species."_protein.fasta");
- if(defined($self->dumpcheck()) and -e $self->ensembl_protein_file() and -e $self->ensembl_dna_file()){
+
+ if(defined($self->dumpcheck()) and -e $ensembl->protein_file() and -e $ensembl->dna_file()){
return;
}
- open(DNA,">".$self->ensembl_dna_file())
- || die("Could not open dna file for writing: ".$self->ensembl_dna_file."\n");
+ open(DNA,">".$ensembl->dna_file())
+ || die("Could not open dna file for writing: ".$ensembl->dna_file."\n");
- open(PEP,">".$self->ensembl_protein_file())
- || die("Could not open protein file for writing: ".$self->ensembl_protein_file."\n");
+ open(PEP,">".$ensembl->protein_file())
+ || die("Could not open protein file for writing: ".$ensembl->protein_file."\n");
my $gene_adaptor = $db->get_GeneAdaptor();
@@ -498,104 +498,60 @@ sub fetch_and_dump_seq{
-#=head2 xref_protein_file
-#
-# Arg [1] : (optional) string $arg
-# the fasta file name for the protein xref
-# Example : $file name = $xref->xref_protein_file();
-# Description: Getter / Setter for the protien xref fasta file
-# Returntype : string
-# Exceptions : none
-#
-#=cut
-#
-#
-#sub xref_protein_file{
-# my ($self, $arg) = @_;
-#
-# (defined $arg) &&
-# ($self->{_xref_prot_file} = $arg );
-# return $self->{_xref_prot_file};
-#}
-#
-#=head2 xref_dna_file
-#
-# Arg [1] : (optional) string $arg
-# the fasta file name for the dna xref
-# Example : $file name = $xref->xref_dna_file();
-# Description: Getter / Setter for the dna xref fasta file
-# Returntype : string
-# Exceptions : none
-#
-#=cut
-#
-#sub xref_dna_file{
-# my ($self, $arg) = @_;
-#
-# (defined $arg) &&
-# ($self->{_xref_dna_file} = $arg );
-# return $self->{_xref_dna_file};
-#}
-=head2 ensembl_protein_file
+
+=head2 method
- Arg [1] : (optional) string $arg
- the fasta file name for the ensembl proteins
- Example : $file_name = $self->ensembl_protein_file();
- Description: Getter / Setter for the protien ensembl fasta file
- Returntype : string
+ Arg [1] : (optional) list reference $arg
+ reference to a list of method names
+ Example : my @methods = @{$self->method()};
+ Description: Getter / Setter for the methods
+ Returntype : list
Exceptions : none
=cut
-sub ensembl_protein_file{
+
+sub method{
my ($self, $arg) = @_;
(defined $arg) &&
- ($self->{_ens_prot_file} = $arg );
- return $self->{_ens_prot_file};
+ ($self->{_method} = $arg );
+ return $self->{_method};
}
-=head2 ensembl_dna_file
-
- Arg [1] : (optional) string $arg
- the fasta file name for the ensembl dna
- Example : $file_name = $self->ensembl_dna_file();
- Description: Getter / Setter for the protien ensembl fasta file
- Returntype : string
- Exceptions : none
+sub core{
+ my ($self, $arg) = @_;
-=cut
+ (defined $arg) &&
+ ($self->{_core} = $arg );
+ return $self->{_core};
+}
-sub ensembl_dna_file{
+sub dumpcheck {
my ($self, $arg) = @_;
(defined $arg) &&
- ($self->{_ens_dna_file} = $arg );
- return $self->{_ens_dna_file};
+ ($self->{_dumpcheck} = $arg );
+ return $self->{_dumpcheck};
}
-=head2 method
-
- Arg [1] : (optional) list reference $arg
- reference to a list of method names
- Example : my @methods = @{$self->method()};
- Description: Getter / Setter for the methods
- Returntype : list
- Exceptions : none
-
-=cut
+sub maxdump {
+ my ($self, $arg) = @_;
+ (defined $arg) &&
+ ($self->{_maxdump} = $arg );
+ return $self->{_maxdump};
+}
-sub method{
+sub use_existing_mappings {
my ($self, $arg) = @_;
(defined $arg) &&
- ($self->{_method} = $arg );
- return $self->{_method};
+ ($self->{_use_existing_mappings} = $arg );
+ return $self->{_use_existing_mappings};
}
-
sub xref{
my ($self, $arg) = @_;
@@ -622,7 +578,7 @@ sub run_mapping {
# delete old output files in target directory if we're going to produce new ones
if (!defined($self->use_existing_mappings)) {
- my $dir = $self->dir();
+ my $dir = $self->core->dir();
unlink (<$dir/*.map $dir/*.out $dir/*.err>);
}
@@ -651,7 +607,7 @@ sub run_mapping {
$method_target_threshold{$method} = $obj->target_identity_threshold();
if (!defined($self->use_existing_mappings)) {
- my $job_name = $obj->run($queryfile, $targetfile, $self->dir());
+ my $job_name = $obj->run($queryfile, $targetfile, $self->core->dir());
push @job_names, $job_name;
sleep 1; # make sure unique names really are unique
}
@@ -661,7 +617,7 @@ sub run_mapping {
if (!defined($self->use_existing_mappings)) {
# submit depend job to wait for all mapping jobs
- submit_depend_job($self->dir, @job_names);
+ submit_depend_job($self->core->dir, @job_names);
}
} # run_mapping
@@ -766,16 +722,18 @@ sub submit_depend_job {
sub parse_mappings {
- my ($self, $xref) = @_;
+ my ($self) = @_;
- my $dir = $self->dir();
+ my $ensembl = $self->core;
+ my $xref = $self->xref;
+ my $dir = $ensembl->dir();
- # incase timed out.
- $self->dbc->connect();
- $self->xref->dbc->connect();
+ # incase timed out, force reconnection
+ $ensembl->dbc->connect();
+ $xref->dbc->connect();
# get current max object_xref_id
- my $row = @{$self->dbc->db_handle->selectall_arrayref("SELECT MAX(object_xref_id) FROM object_xref")}[0];
+ my $row = @{$ensembl->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";
@@ -786,7 +744,7 @@ sub parse_mappings {
my $object_xref_id_offset = $max_object_xref_id + 1;
my $object_xref_id = $object_xref_id_offset;
- $row = @{$self->dbc->db_handle->selectall_arrayref("SELECT MAX(xref_id) FROM xref")}[0];
+ $row = @{$ensembl->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";
@@ -887,7 +845,7 @@ sub parse_mappings {
print "Read $total_lines lines from $total_files exonerate output files\n";
# write relevant xrefs to file
- my $max_object_xref_id = $self->dump_core_xrefs(\%primary_xref_ids, $object_xref_id+1, $xref_id_offset, $object_xref_id_offset, \%ensembl_object_types);
+ $max_object_xref_id = $self->dump_core_xrefs(\%primary_xref_ids, $object_xref_id+1, $xref_id_offset, $object_xref_id_offset, \%ensembl_object_types);
# dump xrefs that don't appear in either the primary_xref or dependent_xref tables
$self->dump_orphan_xrefs($xref_id_offset);
@@ -913,7 +871,7 @@ sub dump_orphan_xrefs() {
my $count;
- open (XREF, ">>" . $self->dir() . "/xref.txt");
+ open (XREF, ">>" . $self->core->dir() . "/xref.txt");
# 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";
@@ -955,13 +913,13 @@ sub dump_direct_xrefs {
my $count = 0;
- open (XREF, ">>" . $self->dir() . "/xref.txt");
- open (OBJECT_XREF, ">>" . $self->dir() . "/object_xref.txt");
+ open (XREF, ">>" . $self->core->dir() . "/xref.txt");
+ open (OBJECT_XREF, ">>" . $self->core->dir() . "/object_xref.txt");
# 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 = $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");
+ my $trans_sth = $self->core->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);
@@ -1063,7 +1021,7 @@ sub dump_interpro {
my $self = shift;
- open (INTERPRO, ">" . $self->dir() . "/interpro.txt");
+ open (INTERPRO, ">" . $self->core->dir() . "/interpro.txt");
my $sth = $self->xref->dbc->prepare("SELECT * FROM interpro");
$sth->execute();
@@ -1090,7 +1048,7 @@ 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 = $self->dbc->prepare($core_sql);
+ my $sth = $self->core->dbc->prepare($core_sql);
$sth->execute();
my ($internal_id, $stable_id);
$sth->bind_columns(\$internal_id, \$stable_id);
@@ -1152,7 +1110,7 @@ sub get_analysis_id {
my $logic_name = $typeToLogicName{lc($ensembl_type)};
- my $sth = $self->dbc->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
+ my $sth = $self->core->dbc->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
$sth->execute();
my $analysis_id;
@@ -1165,7 +1123,7 @@ sub get_analysis_id {
} else {
print "No analysis with logic_name $logic_name found, creating ...\n";
- $sth = $self->dbc->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
+ $sth = $self->core->dbc->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
# TODO - other fields in analysis table
$sth->execute();
$analysis_id = $sth->{'mysql_insertid'};
@@ -1186,7 +1144,7 @@ sub dump_core_xrefs {
my %xref_to_objects = %$xref_ids_hashref;
my %ensembl_object_types = %$ensembl_object_types_hashref;
- my $dir = $self->dir();
+ my $dir = $self->core->dir();
open (XREF, ">$dir/xref.txt");
open (OBJECT_XREF, ">>$dir/object_xref.txt");
@@ -1350,7 +1308,7 @@ sub dump_comparison {
my $self = shift;
- my $dir = $self->dir();
+ my $dir = $self->core->dir();
print "Dumping comparison data\n";
@@ -1382,7 +1340,7 @@ sub build_transcript_display_xrefs {
my ($self, $xref_id_offset) = @_;
- my $dir = $self->dir();
+ my $dir = $self->core->dir();
# get a list of xref sources; format:
# key: xref_id value: source_name
@@ -1406,7 +1364,7 @@ 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 = $self->dbc->prepare("SELECT translation_id, transcript_id FROM translation");
+ $sth = $self->core->dbc->prepare("SELECT translation_id, transcript_id FROM translation");
$sth->execute();
my ($translation_id, $transcript_id);
@@ -1569,16 +1527,9 @@ sub build_gene_display_xrefs {
my ($self, $transcript_display_xrefs) = @_;
- my $dir = $self->dir();
+ my $dir = $self->core->dir();
-# 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 $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-dbconn => $self->core->dbc);
my $ta = $db->get_TranscriptAdaptor();
@@ -1678,7 +1629,7 @@ sub build_genes_to_transcripts {
print "Getting transcripts for all genes\n";
my $sql = "SELECT gene_id, transcript_id FROM transcript";
- my $sth = $self->dbc->prepare($sql);
+ my $sth = $self->core->dbc->prepare($sql);
$sth->execute();
my ($gene_id, $transcript_id);
@@ -1750,7 +1701,7 @@ 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 = $self->dbc->prepare($sql);
+ my $core_sth = $self->core->dbc->prepare($sql);
$core_sth->execute($source_name);
my @row = $core_sth->fetchrow_array();
@@ -1777,25 +1728,27 @@ sub do_upload {
my ($self, $deleteexisting) = @_;
+ my $ensembl = $self->core;
+ my $core_db = $ensembl->dbc;
# xref.txt etc
# TODO warn if table not empty
foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "gene_description", "go_xref", "interpro") {
- my $file = $self->dir() . "/" . $table . ".txt";
+ my $file = $ensembl->dir() . "/" . $table . ".txt";
my $sth;
if ($deleteexisting) {
- $sth = $self->dbc->prepare("DELETE FROM $table");
+ $sth = $core_db->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 = $self->dbc->prepare("LOAD DATA INFILE \'$file\' IGNORE INTO TABLE $table");
+ $sth = $core_db->prepare("LOAD DATA INFILE \'$file\' IGNORE INTO TABLE $table");
print "Uploading data in $file to $table\n";
$sth->execute();
@@ -1804,22 +1757,23 @@ sub do_upload {
# gene_display_xref.sql etc
foreach my $table ("gene", "transcript") {
- my $file = $self->dir() . "/" . $table . "_display_xref.sql";
+
+ my $file = $ensembl->dir() . "/" . $table . "_display_xref.sql";
my $sth;
if ($deleteexisting) {
- $sth = $self->dbc->prepare("UPDATE $table SET display_xref_id=NULL");
+ $sth = $core_db->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->dbc->dbname() . " < $file";
+ my $str = "mysql -u " .$core_db->user() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
system $str;
- #$sth = $self->dbc->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
+ #$sth = $core_db->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
#open(DX_TXT, $file);
#while (<DX_TXT>) {
# my ($xref_id, $object_id) = split;
@@ -1888,7 +1842,7 @@ sub build_gene_descriptions {
print "Regexp filtering (" . scalar(@regexps) . " regexps) removed $removed descriptions, left with " . scalar(keys %xref_descriptions) . "\n";
- my $dir = $self->dir();
+ my $dir = $self->core->dir();
open(GENE_DESCRIPTIONS,">$dir/gene_description.txt") || die "Could not open $dir/gene_description.txt";
# Foreach gene, get any xrefs associated with its transcripts or translations
@@ -2047,14 +2001,15 @@ sub compare_xref_descriptions {
sub upload_external_db {
my ($self) = @_;
- $self->dbc->connect();
- my $row = @{$self->dbc->db_handle->selectall_arrayref("SELECT COUNT(*) FROM external_db")}[0];
+ my $core_db = $self->core->dbc;
+ $core_db->connect();
+ my $row = @{$core_db->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 = $self->dbc->prepare("LOAD DATA INFILE \'$edb\' INTO TABLE external_db");
+ my $edb_sth = $core_db->prepare("LOAD DATA INFILE \'$edb\' INTO TABLE external_db");
$edb_sth->execute();
} else {
print "external_db table already has $count rows, will not change it\n";
diff --git a/misc-scripts/xref_mapping/XrefMapper/db.pm b/misc-scripts/xref_mapping/XrefMapper/db.pm
index 19f00057d63c0e594a96f18cb68e773852b013be..443f1519c3c1aa9767af03b4353a565cf46eee10 100644
--- a/misc-scripts/xref_mapping/XrefMapper/db.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/db.pm
@@ -1,13 +1,42 @@
package XrefMapper::db;
use vars '@ISA';
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::Utils::ConfigRegistry;
+use Bio::EnsEMBL::DBSQL::DBConnection;
+sub new{
+ my($class, @args) = @_;
-@ISA = qw{Bio::EnsEMBL::DBSQL::DBAdaptor};
+ my $self ={};
+ bless $self,$class;
+ $self->dbc(new Bio::EnsEMBL::DBSQL::DBConnection(@args));
+
+ return $self;
+}
+
+sub species{
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_species} = $arg );
+ return $self->{_species};
+
+}
+
+sub dbc{
+ my $self = shift;
+
+ if(@_){
+ my $arg = shift;
+ if(defined($arg)){
+ if(!$arg->isa('Bio::EnsEMBL::DBSQL::DBConnection')){
+ throw("$arg is no a DBConnection\n");
+ }
+ }
+ $self->{_dbc} = $arg;
+ }
+ return $self->{_dbc};
+}
=head2 dir
@@ -30,28 +59,42 @@ sub dir {
}
-sub dumpcheck {
- my ($self, $arg) = @_;
+=head2 protein_file
+
+ Arg [1] : (optional) string $arg
+ the fasta file name for the ensembl proteins
+ Example : $file_name = $self->ensembl_protein_file();
+ Description: Getter / Setter for the protien ensembl fasta file
+ Returntype : string
+ Exceptions : none
- (defined $arg) &&
- ($self->{_dumpcheck} = $arg );
- return $self->{_dumpcheck};
-}
+=cut
-sub maxdump {
+sub protein_file{
my ($self, $arg) = @_;
(defined $arg) &&
- ($self->{_maxdump} = $arg );
- return $self->{_maxdump};
+ ($self->{_ens_prot_file} = $arg );
+ return $self->{_ens_prot_file};
}
-sub use_existing_mappings {
+=head2 dna_file
+
+ Arg [1] : (optional) string $arg
+ the fasta file name for the ensembl dna
+ Example : $file_name = $self->ensembl_dna_file();
+ Description: Getter / Setter for the protien ensembl fasta file
+ Returntype : string
+ Exceptions : none
+
+=cut
+
+sub dna_file{
my ($self, $arg) = @_;
(defined $arg) &&
- ($self->{_use_existing_mappings} = $arg );
- return $self->{_use_existing_mappings};
+ ($self->{_ens_dna_file} = $arg );
+ return $self->{_ens_dna_file};
}
sub process_dir {
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index b4e334949d7cc797e561264e3c526d6bd011ff4d..37c7ce0ce5912a3bb21e925fc3ad3ff516b9ad45 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -45,7 +45,8 @@ open(FILE, $file) or die("Could not open input file '$file'");
my @all_species;
my $xref=undef;
-my $species=undef;
+my $ensembl=undef;
+my $mapper=undef;
my $type;
my %xref_hash=();
@@ -74,6 +75,7 @@ while( my $line = <FILE> ) {
}
}
+
if(defined($xref_hash{host})){
my ($host, $user, $dbname, $pass, $port);
$host = $xref_hash{'host'};
@@ -143,28 +145,33 @@ if(defined($species_hash{'species'})){
$port = '';
}
- $species = "XrefMapper::$module"->new(-host => $host,
- -port => $port,
- -user => $user,
- -pass => $pass,
- -species => $value,
- -group => 'core',
- -dbname => $dbname);
+
+ $mapper = "XrefMapper::$module"->new();
+
+ my $core = new XrefMapper::db(-host => $host,
+ -port => $port,
+ -user => $user,
+ -pass => $pass,
+ -group => 'core',
+ -dbname => $dbname);
+
if(defined($species_hash{'dir'})){
- $species->dir($species_hash{'dir'});
+ $core->dir($species_hash{'dir'});
}
- $species->species($value);
+ $core->species($value);
+
+ $mapper->core($core);
if(defined($dumpcheck)){
- $species->dumpcheck("yes");
+ $mapper->dumpcheck("yes");
}
if(defined($maxdump)){
- $species->maxdump($maxdump);
+ $mapper->maxdump($maxdump);
}
if(defined($use_existing_mappings)){
- $species->use_existing_mappings("yes");
+ $mapper->use_existing_mappings("yes");
}
@@ -174,22 +181,22 @@ else{
}
-$species->xref($xref); # attach xref object to species object
+$mapper->xref($xref); # attach xref object to mapper object
print "\nDumping xref & Ensembl sequences\n";
-$species->dump_seqs($location);
+$mapper->dump_seqs($location);
print "\nChecking external_db table\n" if ($upload);
-$species->upload_external_db() if ($upload);
+$mapper->upload_external_db() if ($upload);
print "\nRunning mapping\n";
-$species->build_list_and_map();
+$mapper->build_list_and_map();
print "\nParsing mapping output\n";
-$species->parse_mappings();
+$mapper->parse_mappings();
print "\nUploading xrefs\n" if ($upload);
-$species->do_upload($deleteexisting) if ($upload);
+$mapper->do_upload($deleteexisting) if ($upload);
print STDERR "*** All finished ***\n";