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lib/Bio/EnsEMBL/Utils/ConversionSupport.pm  view on Meta::CPAN

  );
  if (! $attrib_id) {
    $self->log_warning("There is no attrib_type_id for code $attrib_code, please patch the attrib_table\n");
    exit;
  }
  else {
    return $attrib_id;
  }
}

=head2 store_new_attribute

  Arg[1]      : seq_region.seq_region_id
  Arg[2]      : attrib_type.code
  Arg[3]      : attrib_type.value
  ARG[4]      : table to update (seq_region_attribute by default)
  Example     : $support->store_new_attribute(23,name,5);
  Description : uses MySQL to store an entry (code and value) in an attribute table 
                (seq_region_attrib by default)
  Return type : array_ref
  Caller      : general
  Status      : stable

=cut

sub store_new_attribute {
  my $self         = shift;
  my $sr_id        = shift;
  my $attrib_code  = shift;
  my $attrib_value = shift || '';
  my $table        = shift || 'seq_region_attrib';

  #get database handle
  my $dbh = $self->get_dbconnection('loutre');
  #get attrib_type_id for this particular attribute
  my $attrib_id = $self->_get_attrib_id($attrib_code,$dbh);
  #store
  my $r = $dbh->do(
    qq(insert into $table
           values (?,?,?)),
    {},
    ($sr_id,$attrib_id,$attrib_value)
  );
  return ['Stored',$r];
}

=head2 update_attribute

  Arg[1]      : seq_region.seq_region_id
  Arg[2]      : attrib_type.code
  Arg[3]      : attrib_type.value
  ARG[4]      : table to update (seq_region_attribute by default)
  Example     : $support->update_attribute(23,name,5);
  Description : uses MySQL to update an attribute table (seq_region_attrib by default)
  Return type : array_ref
  Caller      : general
  Status      : stable

=cut

sub update_attribute {
  my $self = shift;
  my $sr_id = shift;
  my $attrib_code  = shift;
  my $attrib_value = shift;
  my $table        = shift || 'seq_region_attrib';
  my $dbh = $self->get_dbconnection('loutre');
  my $attrib_id = $self->_get_attrib_id($attrib_code,$dbh);
  #update
  my $r = $dbh->do(
    qq(update $table
           set value = ?
           where seq_region_id = $sr_id
           and attrib_type_id = $attrib_id),
    {},
    ($attrib_value)
  );
  return ['Updated',$r];
}


=head2 remove_duplicate_attribs

  Arg[1]      : db handle
  Arg[2]      : table
  Example     : $support->remove_duplicate_attribs($dbh,'gene');
  Description : uses MySQL to remove duplicate entries from an attribute table
  Return type : none
  Caller      : general
  Status      : stable

=cut

sub remove_duplicate_attribs {
  my $self  = shift;
  my $dbh   = shift;
  my $table = shift;
  $dbh->do(qq(create table nondup_${table}_attrib like ${table}_attrib));
  $dbh->do(qq(insert into nondup_${table}_attrib (select ${table}_id, attrib_type_id, value from ${table}_attrib group by ${table}_id, attrib_type_id, value)));
  $dbh->do(qq(delete from ${table}_attrib));
  $dbh->do(qq(insert into ${table}_attrib (select ${table}_id, attrib_type_id, value from nondup_${table}_attrib)));
  $dbh->do(qq(drop table nondup_${table}_attrib));
}

=head2 sav_seq

  Arg[1]      : string (sequence to save)
  Example     : $support->save_seq('ACGT')
  Description : creates a temporary file containing the sequence you give it
  Return type : string (filename)
  Caller      : general
  Status      : stable

=cut

sub save_seq {
  my $self = shift;
  my $content = shift ;
  my $seq_file = $self->param('logpath') . '/SEQ_' . time() . int(rand()*100000000) . $$;
  open (my $fh,">$seq_file", $seq_file) or die("Cannot create working file.$!");
  print $fh $content;