Public Member Functions
public	run ()

Detailed Description

Description

Parse ontology files.  File format (and example data):

   1: DB, database contributing the file (always "TAIR" for this file).
   2: DB_Object_ID  (TAIR's unique identifier for genes).
   3: DB_Object_Symbol, see below
   4: Qualifier (optional), one or more of 'NOT', 'contributes_to',
      'colocalizes_with' as qualifier(s) for a GO annotation, when needed,
      multiples separated by pipe (|)
   5: GO ID, unique numeric identifier for the GO term
   6: DB:Reference(|DB:Reference), the reference associated with the GO
      annotation
   7: Evidence, the evidence code for the GO annotation
   8: With (or) From (optional), any With or From qualifier for the GO
      annotation
   9: Aspect, which ontology the GO term belongs (Function, Process or
      Component)
  10: DB_Object_Name(|Name) (optional), a name for the gene product in
      words, e.g. 'acid phosphatase'
  11: DB_Object_Synonym(|Synonym) (optional), see below
  12: DB_Object_Type, type of object annotated, e.g. gene, protein, etc.
  13: taxon(|taxon), taxonomic identifier of species encoding gene
      product
  14: Date, date GO annotation was made in the format
  15: Assigned_by, source of the annotation (either "TAIR" or "TIGR")

E.g.:
   Field1: TAIR
   Field2: locus:2031476
   Field3: ENO1
   Field4: 
   Field5: GO:0000015
   Field6: TAIR:AnalysisReference:501748310
   Field7: IEA
   Field8: INTERPRO:IPR000941|INTERPRO:IPR020809|INTERPRO:IPR020810|INTERPRO:IPR020811
   Field9: C
  Field10: enolase 1
  Field11: AT1G74030|AT1G74030.1|F2P9.10|F2P9_10
  Field12: protein
  Field13: taxon:3702
  Field14: 20120418
  Field15: TAIR
  Field16: 
  Field17: TAIR:gene:2031475

   Field1: TAIR
   Field2: locus:2081840
   Field3: LTP12
   Field4: 
   Field5: PO:0001009
   Field6: TAIR:Publication:501710265|AGRICOLA_IND:IND23314018
   Field7: IDA
   Field8: 
   Field9: G
  Field10: AT3G51590
  Field11: AT3G51590|LTP12|lipid transfer protein 12|T18N14.1
  Field12: protein
  Field13: taxon:3702
  Field14: 20060215
  Field15: TAIR
  Field16: 
  Field17: TAIR:locus:2081840

Definition at line 72 of file TAIROntologyParser.pm.

Member Function Documentation

◆ run()

public XrefParser::TAIROntologyParser::run ( )

Undocumented method

Code:

click to view

sub run {
    my ($self, $args) = @_;
    my $source_id     = $args->{'source_id'};
    my $species_id    = $args->{'species_id'};
    my $files         = $args->{'files'};
    my $release_file  = $args->{'rel_file'};
    my $notify        = sub { print @_ if $args->{'verbose'} };
 
    unless ( ref $files eq 'ARRAY' ) {
        die '"files" argument not an array?';
    }
 
    my ($ont_file)   = grep { /\.(xml|obo)/ } @$files;
    my ($assoc_file) = grep { $ont_file && !/$ont_file/ } @$files;
 
    if ( $assoc_file ) {
        $notify->(sprintf "%s parsing file '$assoc_file'\n", __PACKAGE__);
    }
    else {
        printf STDERR "%s called without a 'files' argument\n%s", 
            __PACKAGE__, Dumper($args);
        return 1; # error
    }
 
    # get the "main" GO/PO source id.
    my $source_name  = $self->get_source_name_for_source_id( $source_id );
    $source_id = $self->get_source_id_for_source_name( $source_name, 'main' );
 
    #
    # Ontologies are attached to the translations, so this gets all the 
    # translation xrefs as a hash with the translation IDs as the keys
    # and the xref IDs as the values.
    #
    my %master_xrefs = %{ 
        $self->get_valid_codes( $TAIR_TRANSLATION , $species_id ) 
    };
 
    $species_id       ||= $self->get_species_id_for_filename($assoc_file);
    my %species_id2name = $self->species_id2name();
    my $species         = $species_id2name{$species_id}->[0];
 
    $notify->("Parsing $source_name for $species\n");
 
    #
    # Get mappimg from GO terms to descriptions from the XML/OBO file
    #
    #
    my %id_to_term;
    if ( $ont_file ) {
        my $obo_io = $self->get_filehandle( $ont_file );
        if ( !defined $obo_io ) {
            print STDERR "ERROR: Could not open '$ont_file'\n";
            return 1;    # 1 error
        }
 
        my $term = undef;
        my $desc = undef;
 
        if ( $ont_file =~ /\.xml$/ ) { 
            while ( $_ = $obo_io->getline() ) {
                if (/\<id\>([G|P]O:\d+)\<\/id\>/) {
                    $term = $1;
                }
                elsif (/\<name\>(.*)\<\/name\>/) {
                    if ( defined($term) ) {
                        $id_to_term{$term} = $1;
                    }
                    $term = undef;
                }
            }
        }
        else {
            while ( $_ = $obo_io->getline() ) {
                if (/^id:\s+([G|P]O:\d+)/) {
                    $term = $1;
                }
                elsif (/^name:\s+(.*)/) {
                    if ( defined $term ) {
                        $id_to_term{ $term } = $1;
                    }
                    $term = undef;
                }
            }
        }
 
        $obo_io->close();
 
        $notify->(
            sprintf "Mapped %s terms to descriptions\n", 
            scalar keys %id_to_term
        );
    }
 
    my %wrongtype;
 
    my $num_terms  = 0;
    my $count      = 0;
    my $miss_parse = 0;
 
    # Open the gene association GAF file
    my $gaf_io = $self->get_filehandle( $assoc_file );
 
    if ( !defined $gaf_io ) {
        print STDERR "ERROR: Could not open $assoc_file\n";
        return 1; # error
    }
 
    while ( my $line = $gaf_io->getline() ) {
        next if $line =~ /^!/;     # comment
 
        chomp $line;
 
        my @vals = split( /\t/, $line );
        my %rec  = map { $GAF_FIELDS[$_], $vals[$_] } 0..$#GAF_FIELDS;
 
        next if $rec{'db'}        ne 'TAIR'; # Only process TAIR annotations
        next if $rec{'qualifier'} eq 'NOT';  # Skip "NOT" terms entirely
 
        # Find the stable_id(s)
        my @stable_ids = uniq( 
            map  { defined $master_xrefs{ $_ } ? $_ : () }
            grep { /^AT\d+G/ }
            map  { s/\'/\\\'/g; $_ }
            map  { split /[|]/ }
            ( $rec{'db_object_name'}, $rec{'db_object_synonym'} )
        );
 
        if ( !@stable_ids ) {
            $miss_parse++;
            next;
        }
 
        my $ont_id = $rec{'ont_id'};
        my $desc   = $id_to_term{ $ont_id } || '';
 
        for my $stable_id ( @stable_ids ) {
            printf "%-70s\r", sprintf(
                "%10s: %s => %s", ++$num_terms, $ont_id, $stable_id
            );
 
            my @xref_ids = @{ $master_xrefs{ $stable_id } };
 
            for my $xref_id ( @xref_ids ) {
                $self->add_dependent_xref({
                    master_xref_id => $xref_id,
                    acc            => $ont_id,
                    label          => $ont_id,
                    desc           => $desc,
                    linkage        => $rec{'evidence_code'},
                    source_id      => $source_id,
                    species_id     => $species_id 
                });
            }
        }
 
        $count++;
    } 
 
    $gaf_io->close();
 
    $notify->(
        map { " - $_\n" }
        "$count $source_name dependent xrefs added",
        "$miss_parse lines did not contain a recognised stable_id",
    );
 
    if ( defined $release_file ) {
        # Parse and set release information from $release_file.
        my $release_io = $self->get_filehandle($release_file);
 
        # Slurp mode.
        local $/;
        my $release = <$release_io>;
        $release_io->close();
 
        $release =~ tr/\n/ /;
        $release =~ s#.*The following table describes.*?of (POC.*?)<ul>.*#$1#;
        $release =~ s#<[^>]+>##g;
 
        $notify->("$source_name release: '$release'\n");
        $self->set_release( $source_id, $release );
    }
 
    return 0; # success
}

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

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

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ run()