Public Member Functions
public BasicMapper	new ()

public XrefMapper::db	xref ()

public String	farm_queue ()

public String	exonerate ()

public XrefMapper::db	core ()

public XrefMapper::db	previous_core ()

public void	add_meta_pair ()

public	update_process_status ()

public	xref_latest_status ()

public	get_meta_value ()

public	process_file ()

public Scalar	dumpcheck ()

public	nofarm ()

public	verbose ()

public	species_id ()

public	get_id_from_species_name ()

public	get_alt_alleles ()

public	get_official_name ()

public	biomart_fix ()

public	biomart_testing ()

public	biomart_test ()

public	filter_by_regexp ()

public	get_species_id_from_species_name ()

public	clean_up ()

public	remove_mapping_data ()

public	revert_to_parsing_finished ()

public	revert_to_mapping_finished ()

public	get_alt_allele_hashes ()

public	process_alt_alleles ()

public	get_gene_specific_list ()

public	source_defined_move ()

Detailed Description

Definition at line 8 of file BasicMapper.pm.

Member Function Documentation

◆ add_meta_pair()

public void XrefMapper::BasicMapper::add_meta_pair ( )

  Arg [1]    : key
  Arg [2]    : value
  Example    :

$mapper->add_meta_pair("head_directory","/lustre/src/");

  Description: Adds key value pairs to the database
  Returntype : none
  Exceptions : none

Code:

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◆ biomart_fix()

public XrefMapper::BasicMapper::biomart_fix ( )

Undocumented method

Code:

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sub biomart_fix{
  my ($self, $db_name, $type1, $type2, $verbose, $xref_dbc) = @_;
  $xref_dbc = $self->xref->dbc unless defined $xref_dbc;
 
  print "$db_name is associated with both $type1 and $type2 object types\n" if(defined($verbose));
  print "$db_name moved to Gene level.\n" if(!defined($verbose));
 
  my $to;
  my $from;
  my $to_id;
  my $from_id;
  if($type1 eq "Gene" or $type2 eq "Gene"){
    $to = "Gene";
    $to_id = "gene_id";
    if($type1 eq "Translation" or $type2 eq "Translation"){
      $from = "Translation";
      $from_id = "translation_id"
    }
    else{
      $from = "Transcript";
      $from_id = "transcript_id";
    }
  }
  else{
    $to = "Transcript";
    $to_id = "transcript_id";
    $from = "Translation";
    $from_id = "translation_id";
  }
 
  if ($db_name eq 'GO' || $db_name eq 'goslim_goa') { 
    $to = 'Translation';
    $from = 'Transcript';
    $to_id = 'translation_id';
    $from_id = 'transcript_id';
  }
  
  print "Therefore moving all associations from $from to ".$to."\n" if(defined($verbose));
  
 
  my $sql =(<<"EOF");
  UPDATE IGNORE object_xref, gene_transcript_translation, xref, source
    SET object_xref.ensembl_object_type = "$to",
      object_xref.ensembl_id = gene_transcript_translation.$to_id 
    WHERE object_xref.ensembl_object_type = "$from" AND
      object_xref.ensembl_id = gene_transcript_translation.$from_id AND
        xref.xref_id = object_xref.xref_id AND
          xref.source_id = source.source_id AND
                object_xref.ox_status = "DUMP_OUT"  AND
          source.name = "$db_name";
EOF
  my $result =  $xref_dbc->do($sql) ;
 
  if($db_name eq "GO" || $db_name eq 'goslim_goa'){
    $sql =(<<"EOF2");
  DELETE object_xref, identity_xref
    FROM object_xref, xref, source, identity_xref
      WHERE object_xref.ensembl_object_type = "$from" AND
        identity_xref.object_xref_id = object_xref.object_xref_id AND
    xref.xref_id = object_xref.xref_id AND
      xref.source_id = source.source_id AND
            object_xref.ox_status = "DUMP_OUT"  AND
          source.name = "$db_name";
EOF2
    
  $result = $xref_dbc->do($sql);  
 
# Special tidying up for transcripts without translation
# The resulting object_xref does not have an ensembl_id to map to
 
    $sql=(<<"EOF4");
  DELETE object_xref, identity_xref
    FROM object_xref, xref, source, identity_xref
      WHERE object_xref.ensembl_object_type = "$to" AND
        identity_xref.object_xref_id = object_xref.object_xref_id AND
        xref.xref_id = object_xref.xref_id AND
          xref.source_id = source.source_id AND
            object_xref.ensembl_id = 0 AND
              object_xref.ox_status = "DUMP_OUT"  AND
                source.name = "$db_name";
EOF4
  }
  else{
    $sql =(<<"EOF3");
  DELETE object_xref, identity_xref
    FROM xref, source, object_xref
      LEFT JOIN identity_xref
        ON identity_xref.object_xref_id = object_xref.object_xref_id
      WHERE object_xref.ensembl_object_type = "$from" AND
    xref.xref_id = object_xref.xref_id AND
      xref.source_id = source.source_id AND
            object_xref.ox_status = "DUMP_OUT"  AND
          source.name = "$db_name";
EOF3
 
  $result = $xref_dbc->do($sql);
  }
#  print "\n$sql\n";
 
  #delete dependent_xref 
  $sql =(<<'EOF4');
  DELETE FROM dependent_xref WHERE object_xref_id NOT IN 
   (SELECT object_xref_id FROM object_xref);
EOF4
  return;
}

◆ biomart_test()

public XrefMapper::BasicMapper::biomart_test ( )

Undocumented method

Code:

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◆ biomart_testing()

public XrefMapper::BasicMapper::biomart_testing ( )

Undocumented method

Code:

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◆ clean_up()

public XrefMapper::BasicMapper::clean_up ( )

Undocumented method

Code:

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◆ core()

public XrefMapper::db XrefMapper::BasicMapper::core ( )

  Arg [1]    : (optional)
  Example    :

$mapper->core($new_core);

  Description: Getter / Setter for the core.
               info for the ensembl core database.
  Returntype : XrefMapper::db
  Exceptions : none

Code:

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◆ dumpcheck()

public Scalar XrefMapper::BasicMapper::dumpcheck ( )

  Arg [1]    : (optional)
  Example    :

$mapper->dumpcheck("yes");

  Description: Getter / Setter for dumpcheck.
               If set the mapper will not dump fasta files
               if they exist already.
  Returntype : scalar
  Exceptions : none

Code:

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◆ exonerate()

public String XrefMapper::BasicMapper::exonerate ( )

  Arg [1]    : (optional)
  Example    :

$mapper->exonerate("/usr/local/exonerate1.1.1");

  Description: Getter / Setter for the exonerate executable with full path.
  Returntype : string
  Exceptions : none

Code:

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◆ farm_queue()

public String XrefMapper::BasicMapper::farm_queue ( )

  Arg [1]    : (optional)
  Example    :

$mapper->farm_queue("long");

  Description: Getter / Setter for the farm queue.
  Returntype : string
  Exceptions : none

Code:

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◆ filter_by_regexp()

public XrefMapper::BasicMapper::filter_by_regexp ( )

Undocumented method

Code:

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◆ get_alt_allele_hashes()

public XrefMapper::BasicMapper::get_alt_allele_hashes ( )

Undocumented method

Code:

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◆ get_alt_alleles()

public XrefMapper::BasicMapper::get_alt_alleles ( )

Undocumented method

Code:

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sub get_alt_alleles {
  my $self =  shift;
  
  my $dba = $self->core->dba;
  my $aaga = Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor->new($dba);
  
  my $aa_list = $aaga->fetch_all();
  
  my $count = scalar(@$aa_list);
  my %alt_id_to_gene_id;
  my %gene_id_to_alt_id;
  my $max_alt_id = 0;
  my %is_reference;
  my $sth;
  my $insert_sth = $self->xref->dbc->prepare("insert into alt_allele (alt_allele_id, gene_id, is_reference) values (?, ?,?)");
 
  if($count){
    $sth = $self->xref->dbc->prepare("delete from alt_allele");
    $sth->execute;
    my $alt_added = 0;
    my $num_of_genes = 0;
    
    # Iterate through all alt-allele groups, pushing unique alleles into the xref alt allele table.
    # Track the reference gene IDs.
    
    foreach my $aag (@$aa_list) {
        my $ref_gene = $aag->rep_Gene_id();
        # Representative gene not guaranteed, try to find an alternative best fit
        if (!$ref_gene) {
            my $genes = $aag->get_all_Genes;
            foreach my $gene (@$genes) {
                if ($gene->slice->is_reference) {
                    $ref_gene = $gene->dbID;
                }
            }
        }
        if (!$ref_gene) { 
            warn('Tried very hard but failed to select a representative gene for alt-allele-group '.$aag->dbID);
            next;
        }
        $is_reference{$ref_gene} = 1;
        my $others = $aag->get_all_Gene_ids('no rep');
        # Extra step in place to handle non-ref situations
        my @cleaned_others = grep {!/$ref_gene/} @$others;
        
        $insert_sth->execute($aag->dbID,$ref_gene,1);
        $num_of_genes++;
        $alt_added++;
        foreach my $aa (@cleaned_others) {
            $insert_sth->execute($aag->dbID,$aa,0);
            $num_of_genes++;
        }
        
        if ($aag->dbID > $max_alt_id) { $max_alt_id = $aag->dbID }
    }
    
    print "$alt_added alleles found containing $num_of_genes genes\n";
  }
  else{
    print "No alt_alleles found for this species.\n" ;
  }
 
 
  ### LRGs added as alt_alleles in the XREF system but never added to core.
 
  #
  # Use $max_alt_id for new ones.
  #
  
  my $sql =(<<'LRG');
SELECT  ox.ensembl_id, g.gene_id
  FROM xref x, object_xref ox, external_db e, gene g
    WHERE x.xref_id = ox.xref_id AND
          e.external_db_id = x.external_db_id AND
          e.db_name like "Ens_Hs_gene" AND
          ox.ensembl_object_type = "Gene" AND
           x.display_label = g.stable_id
LRG
  
  $sth = $self->core->dbc->prepare($sql);
  my ($core_gene_id, $lrg_gene_id);
  $sth->execute();
  $sth->bind_columns(\$lrg_gene_id, \$core_gene_id);
  
  $count =0;
  
  my $old_count = 0;
  my $new_count = 0;
  my $lrg_count = 0;
  #
  # If the core gene is already in an alt_allele set then use that alt_id for the LRG gene only.
  # Else use a new one and add both core and LRG.
  #
  
 
  while ($sth->fetch()){
    my $aag = $aaga->fetch_by_gene_id($core_gene_id);
    if ($aag) {
        $insert_sth->execute($aag->dbID, $lrg_gene_id, 0);
        $old_count++;
    } else {
        $aag = $aaga->fetch_by_gene_id($lrg_gene_id);
        if ($aag) {
            $insert_sth->execute($aag->dbID, $lrg_gene_id, 1);
            print "LRG perculiarity\t$core_gene_id\t$lrg_gene_id\n";
            $lrg_count++;
        } else {
            $max_alt_id++;
            $insert_sth->execute($max_alt_id, $lrg_gene_id, 0);
            $insert_sth->execute($max_alt_id, $core_gene_id, 1);
            $new_count++;
        }
    }
    $count++;
  }
 
  
  if($count){
    print "Added $count alt_allels for the lrgs. $old_count added to previous alt_alleles and $new_count new ones\n";
    print "LRG problem count = $lrg_count\n";
  }
 
 
  $self->update_process_status("alt_alleles_added");
  return;
  
}

◆ get_gene_specific_list()

public XrefMapper::BasicMapper::get_gene_specific_list ( )

Undocumented method

Code:

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◆ get_id_from_species_name()

public XrefMapper::BasicMapper::get_id_from_species_name ( )

Undocumented method

Code:

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◆ get_meta_value()

public XrefMapper::BasicMapper::get_meta_value ( )

Undocumented method

Code:

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◆ get_official_name()

public XrefMapper::BasicMapper::get_official_name ( )

Undocumented method

Code:

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◆ get_species_id_from_species_name()

public XrefMapper::BasicMapper::get_species_id_from_species_name ( )

Undocumented method

Code:

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◆ new()

public BasicMapper XrefMapper::BasicMapper::new ( )

  Description: Constructor for BasicMapper.
  Returntype : BasicMapper
  Exceptions : none
  Caller     : general

Code:

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◆ nofarm()

public XrefMapper::BasicMapper::nofarm ( )

Undocumented method

Code:

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◆ previous_core()

public XrefMapper::db XrefMapper::BasicMapper::previous_core ( )

  Arg [1]    : (optional)
  Example    :

$mapper->previous_core($old_core);

  Description: Getter / Setter for the previous release of the core db.
  Returntype : XrefMapper::db
  Exceptions : none

Code:

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◆ process_alt_alleles()

public XrefMapper::BasicMapper::process_alt_alleles ( )

Undocumented method

Code:

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sub process_alt_alleles{
  my $self = shift;
  my $dbc = shift;
  $dbc = $self->xref->dbc unless defined $dbc;
 
  # ALL are on the Gene level now. This may change but for now it is okay.
  my ($alt_to_ref, $ref_to_alts) = $self->get_alt_allele_hashes();
 
  my $tester = XrefMapper::TestMappings->new($self);
  #
  # Move the xrefs on to the reference Gene.
  # NOTE: Igonore used as the xref might already be on this Gene already and we do not want it to crash
  #
  my $move_sql =(<<'MOVE');
UPDATE IGNORE object_xref ox, xref x, source s 
  SET ox.ensembl_id = ? 
    WHERE x.source_id = s.source_id AND 
          ox.xref_id = x.xref_id AND
          ox.ensembl_id = ? AND
          ox.ensembl_object_type = 'Gene' AND
          ox.ox_status = 'DUMP_OUT' AND 
          s.name in (
MOVE
$move_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
 
print "MOVE SQL\n$move_sql\n";
 
  #
  # Now where it was already on the Gene the ignore will have stopped the move
  # so we now want to just remove those ones as they already exist.
  #
  my $del_ix_sql =(<<'DIX');
DELETE ix 
  FROM identity_xref ix, object_xref ox, xref x, source s 
    WHERE x.source_id = s.source_id AND
          ox.object_xref_id = ix.object_xref_id AND
          ox.xref_id = x.xref_id AND 
          ox.ensembl_id = ? AND 
          ox.ensembl_object_type = 'Gene' AND 
          ox.ox_status = 'DUMP_OUT' AND
           s.name in (
DIX
$del_ix_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
 
  my $del_sql =(<<'DEL');
DELETE ox 
  FROM object_xref ox, xref x, source s 
    WHERE x.source_id = s.source_id AND
          ox.xref_id = x.xref_id AND 
          ox.ensembl_id = ? AND 
          ox.ensembl_object_type = 'Gene' AND 
          ox.ox_status = 'DUMP_OUT' AND
           s.name in (
DEL
$del_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
 
  my $move_sth = $dbc->prepare($move_sql)  || croak "$move_sql cannot be prepared";
  my $del_ix_sth = $dbc->prepare($del_ix_sql)    || croak "$del_ix_sql cannot be prepared";
  my $del_sth = $dbc->prepare($del_sql)    || croak "$del_sql cannot be prepared";
 
  my $move_count = 0;
  my $del_ix_count = 0;
  my $del_ox_count = 0;
  foreach my $key (keys %$alt_to_ref){
    $move_sth->execute($alt_to_ref->{$key}, $key);
    $move_count += $move_sth->rows;
 
    $del_ix_sth->execute($key);
    $del_ix_count += $del_ix_sth->rows;
 
    $del_sth->execute($key);
    $del_ox_count += $del_sth->rows;
  }
  $move_sth->finish;
  $del_sth->finish;
  $del_ix_sth->finish;
 
  print "Number of rows:- moved = $move_count, identitys deleted = $del_ix_count, object_xrefs deleted = $del_ox_count\n";
  #
  # Now we have all the data on the reference Gene we want to copy all the data
  # onto the alt alleles.
  #
 
 
  my $get_data_sql=(<<'GET');
SELECT ox.object_xref_id, ox.ensembl_object_type, ox.xref_id, ox.linkage_annotation, 
       ox.linkage_type, ox.ox_status, ox.unused_priority, ox.master_xref_id,
       ix.query_identity, ix.target_identity, ix.hit_start, ix.hit_end,
       ix.translation_start, ix.translation_end, ix.cigar_line, ix.score, ix.evalue
  FROM xref x, source s, object_xref ox 
    LEFT JOIN identity_xref ix ON ox.object_xref_id =ix.object_xref_id 
      WHERE  x.source_id = s.source_id AND
             ox.xref_id = x.xref_id AND
             ox.ensembl_id = ? AND
             ox.ox_status = 'DUMP_OUT' AND
             ox.ensembl_object_type = 'Gene' AND
              s.name in (
GET
 
  $get_data_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
 
  my $get_data_sth = $self->xref->dbc->prepare($get_data_sql) || croak "Could not prepare $get_data_sql";
 
 
 
  my $insert_object_xref_sql =(<<'INO');
INSERT INTO object_xref (object_xref_id, ensembl_id, ensembl_object_type, xref_id, linkage_annotation, 
            linkage_type, ox_status, unused_priority, master_xref_id) 
       VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
INO
 
  my $insert_ox_sth = $self->xref->dbc->prepare($insert_object_xref_sql) || croak "Could not prepare $insert_object_xref_sql";
 
 
  my $insert_identity_xref_sql = (<<'INI');
INSERT INTO identity_xref (object_xref_id, query_identity, target_identity, hit_start, hit_end,
            translation_start, translation_end, cigar_line, score, evalue ) 
        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
INI
 
  my $insert_ix_sth = $self->xref->dbc->prepare($insert_identity_xref_sql) || croak "Could not prepare $insert_identity_xref_sql";
 
 
 
  my $max_object_xref_id;
 
  my $sth = $self->xref->dbc->prepare("SELECT MAX(object_xref_id) FROM object_xref");
  $sth->execute();
  $sth->bind_columns(\$max_object_xref_id);
  $sth->fetch;
  if((!defined($max_object_xref_id)) or (!$max_object_xref_id)){
    croak "Problem getting max object_xref_id";
  }
  $max_object_xref_id++;
 
  my $added_count = 0;
  my $ignored = 0;
  foreach my $key (keys %$ref_to_alts){
    $get_data_sth->execute($key);
    my ($object_xref_id, $ensembl_object_type, $xref_id, $linkage_annotation,
    $linkage_type, $ox_status, $unused_priority, $master_xref_id,
    $query_identity, $target_identity, $hit_start, $hit_end,
    $translation_start, $translation_end, $cigar_line, $score, $evalue);
 
    $get_data_sth->bind_columns(\$object_xref_id, \$ensembl_object_type, \$xref_id, \$linkage_annotation,
                \$linkage_type, \$ox_status, \$unused_priority, \$master_xref_id,
                \$query_identity, \$target_identity, \$hit_start, \$hit_end,
                \$translation_start, \$translation_end, \$cigar_line, \$score, \$evalue);
 
    while( $get_data_sth->fetch()){
      foreach my $alt (@{$ref_to_alts->{$key}}){
    $max_object_xref_id++;
        $insert_ox_sth->execute($max_object_xref_id, $alt, $ensembl_object_type, $xref_id, $linkage_annotation,
                $linkage_type, $ox_status, $unused_priority, $master_xref_id) || croak "Could not insert object_xref data";
 
#ONLY add identity xref if object_xref was added successfully.
    if( $insert_ox_sth->rows){
      $added_count++;
      $insert_ix_sth->execute($max_object_xref_id, $query_identity, $target_identity, $hit_start, $hit_end,
                $translation_start, $translation_end, $cigar_line, $score, $evalue) ||  croak "Could not insert identity_xref data";
    }
    else{
      $ignored++;
    }
      }
    }
  }
  print "Added $added_count new mapping but ignored $ignored\n";
  
  if($tester->unlinked_entries){
    croak "Problems found after process_alt_alleles\n";
  }
 
  $self->update_process_status('alt_alleles_processed');
  return;
}

◆ process_file()

public XrefMapper::BasicMapper::process_file ( )

Undocumented method

Code:

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sub process_file {
  my $self = shift;
  my $file = shift;
  my $verbose = shift;
  
 
  my $xref=undef;
  my $ensembl=undef;
  my $type;
  
  my %xref_hash=();
  my %species_hash=();
  my %farm_hash=();
  
  open my $fh, "<", $file or croak ("\nCannot open input file '$file':\n $!\n");
  while( my $line = <$fh> ) {
 
    chomp($line);
    next if $line =~ /^#/;
    next if !$line;
 
    my ($key, $value) = split("=",$line);
    $value =~ s/^\s*// if defined $value;
    $value =~ s/\s*$// if defined $value;
    $key =~ s/^\s*// if defined $key;
    $key =~ s/\s*$// if defined $key;
    if($key eq "species"){
      $type = "species";
      $species_hash{'species'} = $value;
    }
    elsif($key eq "xref"){
      $type = "xref";
    }
    elsif($key eq "farm"){
      $type = "farm";
    }
    elsif($type eq "species"){ # processing species data
      $species_hash{lc($key)} = $value;
    }
    elsif($type eq "xref"){    # processing xref data
      $xref_hash{lc($key)} = $value;
    }
    elsif($type eq "farm"){
      $farm_hash{lc($key)} = $value;
    }
  }
  close $fh or croak "Can't close file";
 
  my $value = $species_hash{'species'};
  my $taxon = $species_hash{'taxon'};
 
  if ($value !~ /_/) {
    print STDERR "\'$value\' is not a recognised species - please use full species name (e.g. homo_sapiens) in $file\n";
    exit(1);
  }
 
  my $use_basic = 0;
  my $mapper;
  my $module;
  my $class = "XrefMapper/$value.pm";
  my $eval_test = eval {
    require $class;
  };
  if($@ or $eval_test != 1) {
    if ($@ =~ /Can\'t locate $class/) {
      if (defined $taxon) {
        $class = "XrefMapper/$taxon.pm";
        eval {
      require $class;
        };
        if($@) {
      if ($@ =~ /Can\'t locate $class/)  {
        $use_basic = 1;
      } else { die "$@"; }
        } else {
      $module = $taxon; 
        }
      }
      else {
    $use_basic = 1;
      }
    }
    else {
      die "$@";
    }
 
  } else{
    $module = $value;
  }
 
  if ($use_basic or !defined $module) {
    if(defined($verbose) and $verbose) {
        my $warning_msg = "Did not find a specific mapping module XrefMapper::$value ";
        if (defined $taxon) {
            $warning_msg .= "or XrefMapper::$taxon "; 
        }
        $warning_msg .= "- using XrefMapper::BasicMapper instead\n";
        carp($warning_msg);
    }
        require XrefMapper::BasicMapper;
        $module = "BasicMapper";
  }
 
  $mapper = "XrefMapper::$module"->new();
 
  if(defined($farm_hash{'queue'})){
    $mapper->farm_queue($farm_hash{'queue'});
  }
  if(defined($farm_hash{'exonerate'})){
    $mapper->exonerate($farm_hash{'exonerate'});
  }
 
 
  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{'password'})){
      $pass = $xref_hash{'password'};
    }
    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);
 
    $mapper->xref($xref);
    $mapper->add_meta_pair("xref", $host.":".$dbname);
    if(defined($xref_hash{'dir'})){
      $xref->dir($xref_hash{'dir'});
      if(!-d $xref_hash{'dir'}){
    croak "directory ".$xref_hash{'dir'}." does not exist please create this\n";
      }
    }
    else{
      croak "No directory specified for the xref fasta files\n";
    }
 
  }
  else {
    croak "No host name given for xref database\n";
  }
 
  if(defined($species_hash{'species'})){
 
    my ($host, $port, $user, $dbname, $pass);
    $host = $species_hash{'host'};
    $user = $species_hash{'user'};
    $dbname = $species_hash{'dbname'};
    if(defined($species_hash{'password'})){
      $pass = $species_hash{'password'};
    }
    else{
      $pass = '';
    }
    if(defined($species_hash{'port'})){
      $port = $species_hash{'port'};
    }
    else{
      $port = '';
    }
 
    my $core = new XrefMapper::db(-host => $host,
                  -port => $port,
                  -user => $user,
                  -pass => $pass,
                  -group   => 'core',
                  -dbname => $dbname);
    
    $mapper->core($core);
    
    $mapper->add_meta_pair("species", $host.":".$dbname);
 
    if(defined($species_hash{'dir'})){
       $core->dir($species_hash{'dir'});
       if(!-d $species_hash{'dir'}){
      croak "directory ".$species_hash{'dir'}." does not exist please create this\n";
       }
    }    
    else{
       croak "No directory specified for the ensembl fasta files\n";
    }
    
    $core->species($value);
 
    #connect to previous release of core db if connection details specified in xref_input (pr_host, pr_port, pr_dbname, pr_user) 
    if (defined( $species_hash{'pr_host'}) && defined( $species_hash{'pr_user'}) && defined( $species_hash{'pr_dbname'}) ) {
    my ($pr_host, $pr_port, $pr_user, $pr_dbname);
    $pr_host = $species_hash{'pr_host'};
    $pr_user = $species_hash{'pr_user'};
    $pr_dbname = $species_hash{'pr_dbname'};
    if(defined($species_hash{'pr_port'})){
        $pr_port = $species_hash{'pr_port'};
    }
 
    my $previous_core = new XrefMapper::db(-host => $pr_host,
                  -port => $pr_port,
                  -user => $pr_user,
                  -pass => '',
                  -group   => 'core',
                  -dbname => $pr_dbname);
    
    $mapper->previous_core($previous_core);
 
    $mapper->add_meta_pair("species", $pr_host.":".$pr_dbname);    
 
    }
  }
 
  return $mapper;
}

◆ remove_mapping_data()

public XrefMapper::BasicMapper::remove_mapping_data ( )

Undocumented method

Code:

click to view

◆ revert_to_mapping_finished()

public XrefMapper::BasicMapper::revert_to_mapping_finished ( )

Undocumented method

Code:

click to view

◆ revert_to_parsing_finished()

public XrefMapper::BasicMapper::revert_to_parsing_finished ( )

Undocumented method

Code:

click to view

◆ source_defined_move()

public XrefMapper::BasicMapper::source_defined_move ( )

Undocumented method

Code:

click to view

◆ species_id()

public XrefMapper::BasicMapper::species_id ( )

Undocumented method

Code:

click to view

◆ update_process_status()

public XrefMapper::BasicMapper::update_process_status ( )

Undocumented method

Code:

click to view

◆ verbose()

public XrefMapper::BasicMapper::verbose ( )

Undocumented method

Code:

click to view

◆ xref()

public XrefMapper::db XrefMapper::BasicMapper::xref ( )

  Arg [1]    : (optional)
  Example    :

$mapper->core($new_core);

  Description: Getter / Setter for the core.
               info for the xref database.
  Returntype : XrefMapper::db
  Exceptions : none

Code:

click to view

◆ xref_latest_status()

public XrefMapper::BasicMapper::xref_latest_status ( )

Undocumented method

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ add_meta_pair()

◆ biomart_fix()

◆ biomart_test()

◆ biomart_testing()

◆ clean_up()

◆ core()

◆ dumpcheck()

◆ exonerate()

◆ farm_queue()

◆ filter_by_regexp()

◆ get_alt_allele_hashes()

◆ get_alt_alleles()

◆ get_gene_specific_list()

◆ get_id_from_species_name()

◆ get_meta_value()

◆ get_official_name()

◆ get_species_id_from_species_name()

◆ new()

◆ nofarm()

◆ previous_core()

◆ process_alt_alleles()

◆ process_file()

◆ remove_mapping_data()

◆ revert_to_mapping_finished()

◆ revert_to_parsing_finished()

◆ source_defined_move()

◆ species_id()

◆ update_process_status()

◆ verbose()

◆ xref()

◆ xref_latest_status()