Gramene various ontologies parser

misc-scripts/xref_mapping/XrefParser/GrameneOntologyParser.pm

+package XrefParser::GrameneOntologyParser;
+
+=pod
+
+=head1 NAME
+
+XrefParser::GrameneOntologyParser
+
+=head1 DESCRIPTION
+
+Parse ontology files.  File format (and example data):
+
+ 1: DB, database contributing the file 
+ 2: DB_Object_ID (gene stable id)
+ 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: Ontology accession, e.g., "PO:0007633"
+ 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")
+
+TAIR
+locus:2007106
+EXPA1
+
+PO:0000293
+TAIR:Publication:501680952
+NAS
+
+S
+AT1G69530
+AT1G69530|ATEXPA1|EXP1|AT-EXP1|ATEXP1|ATHEXP ALPHA 1.2|EXPA1|expansin A1|EXPANSIN 1|F10D13.18|F10D13_18
+protein
+taxon:3702
+20040428
+TAIR
+
+TAIR:locus:2007106
+
+=head1 AUTHOR
+
+Ken Youens-Clark E<lt>kclark@cshl.eduE<gt>.
+
+=cut
+
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+
+use base qw( XrefParser::BaseParser );
+
+# Creates ontology xrefs from a GAF annotation file.
+# Also requires an OBO file mapping IDs to terms.
+# The ontology xrefs are dependent on xrefs 
+
+#----------------------------------------------------------------------
+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'} };
+    my $file          = ref $files eq 'ARRAY' ? shift @$files : '';
+
+    if ( $file ) {
+        $notify->(sprintf "%s parsing file '$file'\n", __PACKAGE__);
+    }
+    else {
+        printf STDERR "%s called without a 'files' argument\n%s", 
+            __PACKAGE__, Dumper($args);
+        return 1; # error
+    }
+
+
+    # get the 'PO' or 'GO' source_name
+    my $source_name = $self->get_source_name_for_source_id($source_id);
+
+    # get the "main" GO/PO source id.
+    $source_id = $self->get_source_id_for_source_name( $source_name, 'main' );
+
+    $species_id       ||= $self->get_species_id_for_filename($file);
+    my %species_id2name = $self->species_id2name();
+    my $species         = $species_id2name{$species_id}->[0];
+
+    $notify->("Parsing $source_name for $species\n");
+
+    # These Ontology xrefs depend on gene ID xrefs (TAIR_LOCUS) having been
+    # previously loaded - get the source.
+    my $gene_source_id = $self->get_source_id_for_source_name('TAIR_LOCUS');
+
+    #
+    # Get mappimg from GO terms to descriptions from the obo file.
+    #
+    # The gene_association file in GAF format
+    # http://www.geneontology.org/GO.format.gaf-2_0.shtml
+
+    # The obo file (xml or plain)
+    my %id_to_term;
+    if ( my $file_desc = shift @$files ) {
+        my $obo_io = $self->get_filehandle($file_desc);
+        if ( !defined $obo_io ) {
+            print STDERR "ERROR: Could not open $file_desc\n";
+            return 1;    # 1 error
+        }
+
+        my $term = undef;
+        my $desc = undef;
+
+        if ( $file_desc =~ /xml/ ) {    # xml file format
+            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;
+
+    # Get a list of taxon IDs given that some species have multiple e.g. strains
+    my %sp2tax  = $self->species_id2taxonomy();
+    my @tax_ids = @{ $sp2tax{ $species_id } };
+
+    # Loop for each taxon
+    my $count         = 0;
+    my $miss_parse    = 0;
+    my $miss_get_xref = 0;
+
+    for my $tax_id ( @tax_ids ) {
+        $notify->("processing for taxon: $tax_id\n");
+        my $taxon_line = "taxon:" . $tax_id;
+
+        # Open the gene association GAF file
+        my $gaf_io = $self->get_filehandle( $file );
+
+        if ( !defined $gaf_io ) {
+            print STDERR "ERROR: Could not open $file\n";
+            return 1; # error
+        }
+
+        while ( my $line = $gaf_io->getline() ) {
+            next if $line =~ /^!/;     # comment
+            # next unless /$taxon_line/; # only process data for this taxon
+
+            chomp;
+            my (
+                $DB,                 $DB_Object_ID,
+                $DB_Object_Symbol,   $Qualifier,
+                $GO_ID,              $DB_Reference,
+                $Evidence_Code,      $With,
+                $Aspect,             $DB_Object_Name,
+                $DB_Object_Synonym,  $DB_Object_Type,
+                $Taxon,              $Date,
+                $Assigned_By,        $Annotation_Extension,
+                $Gene_Product_Form_ID, @extra
+            ) = split( /\t/, $line );
+
+            # next unless $Taxon eq $taxon_line;   # Only process this species
+            next if $Qualifier eq "NOT";         # Skip "NOT" terms entirely
+
+            $DB_Object_Name =~ s/\'/\\\'/g;
+            my $master = 0;
+
+            # in po file stable_id=$array[9] # in GO asso file, stable_id=
+            # ??[9] [10]
+
+            # Find the stable_id in either DB_Object_Name or DB_Object_Synonym
+            if ( my $stable_id = $DB_Object_Name || $DB_Object_Synonym ) {
+                my $xref_id = $self->add_xref({
+                    acc           => $stable_id, 
+                    label         => '', 
+                    desc          => $nasc_gene_id, 
+                    source_id     => $nascg_source_id, 
+                    species_id    => $species_id, 
+                    info_type     => 'DIRECT',
+                });
+
+                $self->add_direct_xref( 
+                    $tairg_xref_id, $gene_stable_id, 'Gene', 'DIRECT' 
+                );
+            $count++;
+        } 
+
+        $gaf_io->close();
+    }
+
+    $notify->(
+        map { " - $_\n" }
+        "$count $source_name dependent xrefs added",
+        "$miss_parse lines did not contain a recognised stable_id",
+        "$miss_get_xref lines contained a stable_id that did not " .
+            "correspond with a known xref",
+    );
+
+    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
+}
+
+1;