Script to check if GO ID exists in association with Gene ID

config.yaml

database:
    dsn: "dbi:Oracle:"
    user: ''
    passwd: ''

GAFLoader.pl

package GAFLoader;

use strict;
use warnings;

use Bio::Chado::Schema;
use IO::String;
use LWP::UserAgent;
use Moose;
use MooseX::Attribute::Dependent;
use YAML::Tiny;

with 'MooseX::Getopt';

has '_ebi_base_url' => (
    is      => 'ro',
    isa     => 'Str',
    default => 'http://www.ebi.ac.uk/QuickGO/GAnnotation?format=gaf&protein='
);

has '_ua' => (
    is      => 'ro',
    isa     => 'LWP::UserAgent',
    default => sub { LWP::UserAgent->new },
    lazy    => 1
);

has 'schema' => (
    is         => 'rw',
    isa        => 'Bio::Chado::Schema',
    dependency => All [ '_dsn', '_user', '_passwd' ]
);

has 'config_file' => (
    is      => 'rw',
    isa     => 'Str',
    trigger => sub {
        my ($self) = @_;
        my $conf = YAML::Tiny->read( $self->config_file );
        $self->_dsn( $conf->[0]->{database}->{dsn} );
        $self->_user( $conf->[0]->{database}->{user} );
        $self->_passwd( $conf->[0]->{database}->{passwd} );
        $self->schema(
            Bio::Chado::Schema->connect(
                $self->_dsn, $self->_user,
                $self->_passwd, { LongReadLen => 2**25 }
            )
        );
    },
    required => 1
);

has [qw/_dsn _user _passwd/] => (
    is         => 'rw',
    isa        => 'Str',
    default    => "",
    lazy       => 1,
    dependency => All ['config_file']
);

sub parse_go_from_gaf {
    my ( $self, $gaf ) = @_;
    my @go_new;
    my $io = IO::String->new();
    $io->open($gaf);
    while ( my $line = $io->getline ) {
        chomp($line);
        next if $line =~ /^!/;
        my @row_vals = split( "\t", $line );
        print $row_vals[4] . "\n";
        push( @go_new, $row_vals[4] );
    }
    return @go_new;
}

sub get_go_for_gene {
    my ( $self, $gene_id ) = @_;
    my $go_rs = $self->schema->resultset('Sequence::Feature')->search(

    );
}

sub get_gaf_from_ebi {
    my ( $self, $gene_id ) = @_;
    my $response
        = $self->_ua->get( $self->_ebi_base_url . $gene_id )->decoded_content;
    return $response;
}

sub compare_go {

}

sub run {
    my ($self) = @_;
    my $gene_rs = $self->schema->resultset('Sequence::Feature')->search(
        {   'type.name'            => 'gene',
            'organism.common_name' => 'dicty'
        },
        {   join     => [qw/type organism/],
            select   => [qw/feature_id uniquename/],
            prefetch => 'dbxref'
        }
    );
    while ( my $gene = $gene_rs->next ) {
        my $gaf      = $self->get_gaf_from_ebi( $gene->dbxref->accession ); # Get GAF from EBI for given Gene ID
        my @go_new   = $self->parse_go_from_gaf($gaf); # Get GO IDs in an array for a given GAF of a Gene ID
        my @go_exist = $self->get_go_for_gene( $gene->dbxref->accession ); # Query using BCS to check what GO IDs are associated with given Gene ID
        $self->compare_go( @go_new, @go_exist );
    }
}

1;

package main;
GAFLoader->new_with_options->run;

GO_for_GeneId.sql

SELECT GENE_ID.accession gene_id, GENE.uniquename gene, 'GO' || ':' || GO_ID.accession go_id
FROM feature_cvterm fcvt

JOIN feature GENE ON GENE.feature_id = fcvt.feature_id
JOIN dbxref GENE_ID ON GENE_ID.dbxref_id = GENE.dbxref_id
JOIN cvterm type ON type.cvterm_id = GENE.type_id

JOIN cvterm GO ON GO.cvterm_id = fcvt.cvterm_id 
JOIN cv ON cv.cv_id = GO.cv_id
JOIN dbxref GO_ID ON GO_ID.dbxref_id = GO.dbxref_id
JOIN db ON db.db_id = GO_ID.db_id

JOIN organism ON organism.organism_id = GENE.organism_id

WHERE cv.name IN('molecular_function',   'biological_process',   'cellular_component')
AND organism.common_name = 'dicty'
AND db.name = 'GO'
AND GO.is_obsolete = 0
AND GENE.uniquename = 'mhcA'
/* GENE_ID.accession = '' */
ORDER BY GO_ID.accession, GENE_ID.accession ASC
;

To run the script, fill up the required valies in config.yaml; then

perl GAFLoader.pl --config_file config.yaml