Public Member Functions
public	new ()

public	dbi ()

public	get_filehandle ()

public	get_source_id_for_source_name ()

public	get_source_ids_for_source_name_pattern ()

public	get_source_name_for_source_id ()

public	get_valid_xrefs_for_dependencies ()

public	get_valid_xrefs_for_direct_xrefs ()

public	label_to_acc ()

public	get_valid_codes ()

public	upload_xref_object_graphs ()

public	upload_direct_xrefs ()

public	add_meta_pair ()

public	get_xref_sources ()

public	species_id2taxonomy ()

public	species_id2name ()

public	get_xref_id ()

public	primary_xref_id_exists ()

public	get_taxonomy_from_species_id ()

public	get_direct_xref ()

public	get_xref ()

public	get_object_xref ()

public	add_xref ()

public	add_object_xref ()

public	add_identity_xref ()

public	add_to_direct_xrefs ()

public	add_direct_xref ()

public	add_dependent_xref ()

public	add_dependent_xref_maponly ()

public	add_to_syn_for_mult_sources ()

public	add_to_syn ()

public	add_synonym ()

public	get_label_to_acc ()

public	get_acc_to_label ()

public	get_label_to_desc ()

public	set_release ()

public	get_dependent_mappings ()

public	get_ext_synonyms ()

public	parsing_finished_store_data ()

public	get_meta_value ()

protected	_update_xref_info_type ()

Detailed Description

Definition at line 8 of file BaseParser.pm.

Member Function Documentation

◆ _update_xref_info_type()

protected XrefParser::BaseParser::_update_xref_info_type ( )

Undocumented method

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◆ add_dependent_xref()

public XrefParser::BaseParser::add_dependent_xref ( )

Undocumented method

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sub add_dependent_xref{
  my ($self, $arg_ref) = @_;
 
  my $master_xref = $arg_ref->{master_xref_id} || croak( 'Need a master_xref_id on which this xref depends on' );
  my $acc         = $arg_ref->{acc}            || croak( 'Need an accession of this dependent xref' );
  my $source_id   = $arg_ref->{source_id}      || croak( 'Need a source_id for this dependent xref' );
  my $species_id  = $arg_ref->{species_id}     || croak( 'Need a species_id for this dependent xref' );
  my $version     = $arg_ref->{version}        // 0;
  my $label       = $arg_ref->{label}          // $acc;
  my $description = $arg_ref->{desc};
  my $linkage     = $arg_ref->{linkage};
  my $info_text   = $arg_ref->{info_text}      // q{};
  my $dbi         = $arg_ref->{dbi};
 
  $dbi = $self->dbi unless defined $dbi;
 
  my $sql = (<<'IXR');
INSERT INTO xref
  (accession,version,label,description,source_id,species_id, info_type, info_text)
  VALUES (?,?,?,?,?,?,?,?)
IXR
  my $add_xref_sth = $dbi->prepare($sql);
 
  ####################################################
  # Does the xref already exist. If so get its xref_id
  # else create it and get the new xref_id
  ####################################################
  my $dependent_id = $self->get_xref($acc, $source_id, $species_id, $dbi);
  if(!(defined $dependent_id)){
    $add_xref_sth->execute(
        $acc, $version, $label,
        $description, $source_id, $species_id, 'DEPENDENT', $info_text
    ) or croak("$acc\t$label\t\t$source_id\t$species_id\n");
  }
  $add_xref_sth->finish();
 
  ################################################
  # Croak if we have failed to create/get the xref
  ################################################
  $dependent_id = $self->get_xref($acc, $source_id, $species_id, $dbi);
  if ( !$dependent_id ) {
    croak("$acc\t$label\t\t$source_id\t$species_id\n");
  }
 
  ################################
  # Now add the dependency mapping
  ################################
  $self->add_dependent_xref_maponly( $dependent_id, $source_id,
                                     $master_xref, $linkage,
                                     $dbi );
 
  return $dependent_id;
}

◆ add_dependent_xref_maponly()

public XrefParser::BaseParser::add_dependent_xref_maponly ( )

Undocumented method

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◆ add_direct_xref()

public XrefParser::BaseParser::add_direct_xref ( )

Undocumented method

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◆ add_identity_xref()

public XrefParser::BaseParser::add_identity_xref ( )

Undocumented method

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◆ add_meta_pair()

public XrefParser::BaseParser::add_meta_pair ( )

Undocumented method

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◆ add_object_xref()

public XrefParser::BaseParser::add_object_xref ( )

Undocumented method

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◆ add_synonym()

public XrefParser::BaseParser::add_synonym ( )

Undocumented method

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◆ add_to_direct_xrefs()

public XrefParser::BaseParser::add_to_direct_xrefs ( )

Undocumented method

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◆ add_to_syn()

public XrefParser::BaseParser::add_to_syn ( )

Undocumented method

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◆ add_to_syn_for_mult_sources()

public XrefParser::BaseParser::add_to_syn_for_mult_sources ( )

Undocumented method

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◆ add_xref()

public XrefParser::BaseParser::add_xref ( )

Undocumented method

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sub add_xref {
  my ( $self, $arg_ref) = @_;
 
  my $acc         = $arg_ref->{acc}        || croak 'add_xref needs aa acc';
  my $source_id   = $arg_ref->{source_id}  || croak 'add_xref needs a source_id';
  my $species_id  = $arg_ref->{species_id} || croak 'add_xref needs a species_id';
  my $label       = $arg_ref->{label}      // $acc;
  my $description = $arg_ref->{desc};
  my $version     = $arg_ref->{version}    // 0;
  my $info_type   = $arg_ref->{info_type}  // 'MISC';
  my $info_text   = $arg_ref->{info_text}  // q{};
  my $dbi         = $arg_ref->{dbi};
 
  $dbi = $self->dbi unless defined $dbi;
 
  ##################################################################
  # See if it already exists. It so return the xref_id for this one.
  ##################################################################
  my $xref_id = $self->get_xref($acc,$source_id, $species_id, $dbi);
  if(defined $xref_id){
    return $xref_id;
  }
 
  my $add_xref_sth =
      $dbi->prepare( 'INSERT INTO xref '
         . '(accession,version,label,description,source_id,species_id, info_type, info_text) '
         . 'VALUES(?,?,?,?,?,?,?,?)' );
 
  ######################################################################
  # If the description is more than 255 characters, chop it off and add
  # an indication that it has been truncated to the end of it.
  ######################################################################
  if (defined $description && ((length $description) > 255 ) ) {
    my $truncmsg = ' /.../';
    substr $description, 255 - (length $truncmsg),
            length $truncmsg, $truncmsg;
  }
 
 
  ####################################
  # Add the xref and croak if it fails
  ####################################
  $add_xref_sth->execute( $acc, $version || 0, $label,
                          $description, $source_id, $species_id, $info_type, $info_text
  ) or croak("$acc\t$label\t\t$source_id\t$species_id\n");
 
  $add_xref_sth->finish();
  return $add_xref_sth->{'mysql_insertid'};
} ## end sub add_xref

◆ dbi()

public XrefParser::BaseParser::dbi ( )

Undocumented method

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◆ get_acc_to_label()

public XrefParser::BaseParser::get_acc_to_label ( )

Undocumented method

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◆ get_dependent_mappings()

public XrefParser::BaseParser::get_dependent_mappings ( )

Undocumented method

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◆ get_direct_xref()

public XrefParser::BaseParser::get_direct_xref ( )

Undocumented method

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◆ get_ext_synonyms()

public XrefParser::BaseParser::get_ext_synonyms ( )

Undocumented method

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◆ get_filehandle()

public XrefParser::BaseParser::get_filehandle ( )

Undocumented method

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◆ get_label_to_acc()

public XrefParser::BaseParser::get_label_to_acc ( )

Undocumented method

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◆ get_label_to_desc()

public XrefParser::BaseParser::get_label_to_desc ( )

Undocumented method

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◆ get_meta_value()

public XrefParser::BaseParser::get_meta_value ( )

Undocumented method

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◆ get_object_xref()

public XrefParser::BaseParser::get_object_xref ( )

Undocumented method

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◆ get_source_id_for_source_name()

public XrefParser::BaseParser::get_source_id_for_source_name ( )

Undocumented method

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◆ get_source_ids_for_source_name_pattern()

public XrefParser::BaseParser::get_source_ids_for_source_name_pattern ( )

Undocumented method

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◆ get_source_name_for_source_id()

public XrefParser::BaseParser::get_source_name_for_source_id ( )

Undocumented method

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◆ get_taxonomy_from_species_id()

public XrefParser::BaseParser::get_taxonomy_from_species_id ( )

Undocumented method

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◆ get_valid_codes()

public XrefParser::BaseParser::get_valid_codes ( )

Undocumented method

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◆ get_valid_xrefs_for_dependencies()

public XrefParser::BaseParser::get_valid_xrefs_for_dependencies ( )

Undocumented method

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◆ get_valid_xrefs_for_direct_xrefs()

public XrefParser::BaseParser::get_valid_xrefs_for_direct_xrefs ( )

Undocumented method

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◆ get_xref()

public XrefParser::BaseParser::get_xref ( )

Undocumented method

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◆ get_xref_id()

public XrefParser::BaseParser::get_xref_id ( )

Undocumented method

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◆ get_xref_sources()

public XrefParser::BaseParser::get_xref_sources ( )

Undocumented method

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◆ label_to_acc()

public XrefParser::BaseParser::label_to_acc ( )

Undocumented method

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◆ new()

public XrefParser::BaseParser::new ( )

Undocumented method

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◆ parsing_finished_store_data()

public XrefParser::BaseParser::parsing_finished_store_data ( )

Undocumented method

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◆ primary_xref_id_exists()

public XrefParser::BaseParser::primary_xref_id_exists ( )

Undocumented method

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◆ set_release()

public XrefParser::BaseParser::set_release ( )

Undocumented method

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◆ species_id2name()

public XrefParser::BaseParser::species_id2name ( )

Undocumented method

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◆ species_id2taxonomy()

public XrefParser::BaseParser::species_id2taxonomy ( )

Undocumented method

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◆ upload_direct_xrefs()

public XrefParser::BaseParser::upload_direct_xrefs ( )

Undocumented method

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◆ upload_xref_object_graphs()

public XrefParser::BaseParser::upload_xref_object_graphs ( )

Undocumented method

Code:

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sub upload_xref_object_graphs {
  my ($self, $rxrefs, $dbi) = @_;
 
  my $count = scalar @{$rxrefs};
  if($verbose) {
    print "count = $count\n" || croak 'Could not print out count';
  }
 
  if ($count) {
 
    #################
    # upload new ones
    ##################
    if ($verbose) {
      print "Uploading xrefs\n"
    || croak 'Could not print string';
    }
 
 
    #################################################################################
    # Start of sql needed to add xrefs, primary_xrefs, synonym, dependent_xrefs etc..
    #################################################################################
    $dbi = $self->dbi unless defined $dbi;
    my $xref_sth = $dbi->prepare('INSERT INTO xref (accession,version,label,description,source_id,species_id, info_type) VALUES(?,?,?,?,?,?,?)');
    my $pri_insert_sth = $dbi->prepare('INSERT INTO primary_xref VALUES(?,?,?,?)');
    my $pri_update_sth = $dbi->prepare('UPDATE primary_xref SET sequence=? WHERE xref_id=?');
    my $syn_sth = $dbi->prepare('INSERT IGNORE INTO synonym ( xref_id, synonym ) VALUES(?,?)');
    my $xref_update_label_sth = $dbi->prepare('UPDATE xref SET label=? WHERE xref_id=?');
    my $xref_update_descr_sth = $dbi->prepare('UPDATE xref SET description=? WHERE xref_id=?');
    my $pair_sth = $dbi->prepare('INSERT INTO pairs VALUES(?,?,?)');
    my $xref_id_sth = $dbi->prepare("SELECT xref_id FROM xref WHERE accession = ? AND source_id = ? AND species_id = ?");
    my $primary_xref_id_sth = $dbi->prepare('SELECT xref_id FROM primary_xref WHERE xref_id=?');
 
 
 
    # disable error handling here as we'll do it ourselves
    # reenabled it, as errorcodes are really unhelpful
    $xref_sth->{RaiseError} = 0;
    $xref_sth->{PrintError} = 0;
 
    #################################################################################
    # End of sql needed to add xrefs, primary_xrefs, synonym, dependent_xrefs etc..
    #################################################################################
 
 
    foreach my $xref (@{$rxrefs}) {
       my ($xref_id, $direct_xref_id);
       if(!(defined $xref->{ACCESSION} )){
     print "Your xref does not have an accession-number,so it can't be stored in the database\n"
       || croak 'Could not write message';
     return;
       }
 
       ########################################
       # Create entry in xref table and note ID
       ########################################
       if(! $xref_sth->execute($xref->{ACCESSION},
             $xref->{VERSION} || 0,
             $xref->{LABEL}|| $xref->{ACCESSION},
             $xref->{DESCRIPTION},
             $xref->{SOURCE_ID},
             $xref->{SPECIES_ID},
             $xref->{INFO_TYPE} || 'MISC')){
     #
     #  if we failed to add the xref it must already exist so go find the xref_id for this
     #
     if(!(defined $xref->{SOURCE_ID})){
       print "your xref: $xref->{ACCESSION} does not have a source-id\n";
       return;
     }
         $xref_id_sth->execute(
                   $xref->{ACCESSION},
                   $xref->{SOURCE_ID},
                   $xref->{SPECIES_ID} );
         $xref_id = ($xref_id_sth->fetchrow_array())[0];
     if(defined $xref->{LABEL} ) {
       $xref_update_label_sth->execute($xref->{LABEL},$xref_id) ;
     }
     if(defined $xref->{DESCRIPTION} ){
       $xref_update_descr_sth->execute($xref->{DESCRIPTION},$xref_id);
     }
       }
       else{
         $xref_id_sth->execute(
                   $xref->{ACCESSION},
                   $xref->{SOURCE_ID},
                   $xref->{SPECIES_ID} );
         $xref_id = ($xref_id_sth->fetchrow_array())[0];
       }
 
       foreach my $direct_xref (@{$xref->{DIRECT_XREFS}}) {
         $xref_sth->execute( $xref->{ACCESSION},
                             $xref->{VERSION} || 0,
                             $xref->{LABEL} || $xref->{ACCESSION},
                             $xref->{DESCRIPTION},
                             $direct_xref->{SOURCE_ID},
                             $xref->{SPECIES_ID},
                             $direct_xref->{LINKAGE_TYPE});
         $xref_id_sth->execute(
                   $xref->{ACCESSION},
                   $direct_xref->{SOURCE_ID},
                   $xref->{SPECIES_ID} );
         $direct_xref_id = ($xref_id_sth->fetchrow_array())[0];
         $self->add_direct_xref($direct_xref_id, $direct_xref->{STABLE_ID}, $direct_xref->{ENSEMBL_TYPE},$direct_xref->{LINKAGE_TYPE}, $dbi);
       }
 
       ################
       # Error checking
       ################
       if(!((defined $xref_id) and $xref_id)){
     print STDERR "xref_id is not set for :\n".
       "$xref->{ACCESSION}\n$xref->{LABEL}\n".
         "$xref->{DESCRIPTION}\n$xref->{SOURCE_ID}\n".
           "$xref->{SPECIES_ID}\n";
       }
 
 
       #############################################################################
       # create entry in primary_xref table with sequence; if this is a "cumulative"
       # entry it may already exist, and require an UPDATE rather than an INSERT
       #############################################################################
       if(defined $xref->{SEQUENCE} ){
         $primary_xref_id_sth->execute($xref_id) or croak( $dbi->errstr() );
         my @row = $primary_xref_id_sth->fetchrow_array();
         my $exists = $row[0];
     if ( $exists ) {
       $pri_update_sth->execute( $xref->{SEQUENCE}, $xref_id )
         or croak( $dbi->errstr() );
     } else {
       $pri_insert_sth->execute( $xref_id, $xref->{SEQUENCE},
                     $xref->{SEQUENCE_TYPE},
                     $xref->{STATUS} )
         or croak( $dbi->errstr() );
     }
       }
 
       ##########################################################
       # if there are synonyms, add entries in the synonym table
       ##########################################################
       foreach my $syn ( @{ $xref->{SYNONYMS} } ) {
     $syn_sth->execute( $xref_id, $syn )
       or croak( $dbi->errstr() . "\n $xref_id\n $syn\n" );
       }
 
       #######################################################################
       # if there are dependent xrefs, add xrefs and dependent xrefs for them
       #######################################################################
     DEPENDENT_XREF:
       foreach my $depref (@{$xref->{DEPENDENT_XREFS}}) {
         my %dep = %{$depref};
 
         #####################################
         # Insert the xref and get its xref_id
         #####################################
         # print "inserting $dep{ACCESSION},$dep{VERSION},$dep{LABEL},$dep{DESCRIPTION},$dep{SOURCE_ID},${\$xref->{SPECIES_ID}}\n";
         my $dep_xref_id = $self->add_xref({
                                            'acc'        => $dep{ACCESSION},
                                            'source_id'  => $dep{SOURCE_ID},
                                            'species_id' => $xref->{SPECIES_ID},
                                            'label'      => $dep{LABEL},
                                            'desc'       => $dep{DESCRIPTION},
                                            'version'    => $dep{VERSION},
                                            'info_type'  => 'DEPENDENT',
                                            'dbi'        => $dbi,
                                          });
         if( ! $dep_xref_id ) {
           next DEPENDENT_XREF;
         }
 
         #
         # Add the linkage_annotation and source id it came from
         #
         $self->add_dependent_xref_maponly( $dep_xref_id,
                                            $dep{LINKAGE_SOURCE_ID},
                                            $xref_id,
                                            $dep{LINKAGE_ANNOTATION});
 
         #########################################################
         # if there are synonyms, add entries in the synonym table
         #########################################################
         foreach my $syn ( @{ $dep{SYNONYMS} } ) {
           $syn_sth->execute( $dep_xref_id, $syn )
             or croak( $dbi->errstr() . "\n $xref_id\n $syn\n" );
         } # foreach syn
 
       } # foreach dep
 
       #################################################
       # Add the pair data. refseq dna/pep pairs usually
       #################################################
       if(defined $xref_id and defined $xref->{PAIR} ){
     $pair_sth->execute($xref->{SOURCE_ID},$xref->{ACCESSION},$xref->{PAIR});
       }
 
 
       ###########################
       # tidy up statement handles
       ###########################
       if(defined $xref_sth) {$xref_sth->finish()};
       if(defined $pri_insert_sth) {$pri_insert_sth->finish()} ;
       if(defined $pri_update_sth) {$pri_update_sth->finish()};
       if(defined $syn_sth) { $syn_sth->finish()};
       if(defined $xref_update_label_sth) { $xref_update_label_sth->finish()};
       if(defined $xref_update_descr_sth) { $xref_update_descr_sth->finish()};
       if(defined $pair_sth) { $pair_sth->finish()};
       if(defined $xref_id_sth) { $xref_id_sth->finish()};
       if(defined $primary_xref_id_sth) { $primary_xref_id_sth->finish()};
 
     }  # foreach xref
 
  }
  return 1;
}

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

ensembl/misc-scripts/xref_mapping/XrefParser/BaseParser.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ _update_xref_info_type()

◆ add_dependent_xref()

◆ add_dependent_xref_maponly()

◆ add_direct_xref()

◆ add_identity_xref()

◆ add_meta_pair()

◆ add_object_xref()

◆ add_synonym()

◆ add_to_direct_xrefs()

◆ add_to_syn()

◆ add_to_syn_for_mult_sources()

◆ add_xref()

◆ dbi()

◆ get_acc_to_label()

◆ get_dependent_mappings()

◆ get_direct_xref()

◆ get_ext_synonyms()

◆ get_filehandle()

◆ get_label_to_acc()

◆ get_label_to_desc()

◆ get_meta_value()

◆ get_object_xref()

◆ get_source_id_for_source_name()

◆ get_source_ids_for_source_name_pattern()

◆ get_source_name_for_source_id()

◆ get_taxonomy_from_species_id()

◆ get_valid_codes()

◆ get_valid_xrefs_for_dependencies()

◆ get_valid_xrefs_for_direct_xrefs()

◆ get_xref()

◆ get_xref_id()

◆ get_xref_sources()

◆ label_to_acc()

◆ new()

◆ parsing_finished_store_data()

◆ primary_xref_id_exists()

◆ set_release()

◆ species_id2name()

◆ species_id2taxonomy()

◆ upload_direct_xrefs()

◆ upload_xref_object_graphs()