Script to get gene information (DDB-ID, Gene products and Synonyms)

conf.yaml

DB1:
    dsn: dbi:Oracle:host=<hostname>;port=1521;sid=<sid>
    user: <username>
    password: <password>

DB2:
    dsn: dbi:Oracle:host=<hostname>;port=1521;sid=<sid>
    user: <username>
    password: <password>

GeneInfo.pl

use strict;
use warnings;

use Bio::Chado::Schema;
use Bio::DB::SeqFeature::Store;
use Bio::DB::SeqFeature::Store::GFF3Loader;
use YAML::Tiny;

use lib 'lib';
use MOD::SGD;

my $conf     = YAML::Tiny->read('conf.yaml');
my $verbose  = 1;
my $tempFile = File::Temp->new();
my $data_dir = './data';
my $out_file = IO::File->new( 'gene_information.txt', 'w' );

my $gp_schema = MOD::SGD->connect(
    $conf->[0]->{DB1}->{dsn},
    $conf->[0]->{DB1}->{user},
    $conf->[0]->{DB1}->{password}
);

my $syn_schema = Bio::Chado::Schema->connect(
    $conf->[0]->{DB2}->{dsn},
    $conf->[0]->{DB2}->{user},
    $conf->[0]->{DB2}->{password}
);
$syn_schema->source('Sequence::Synonym')->name('synonym_');

my $gene_rs = $syn_schema->resultset('Sequence::Feature')->search(
    {   'type.name'            => 'gene',
        'me.is_deleted'        => 0,
        'organism.common_name' => 'dicty'
    },
    {   join     => [qw/organism type/],
        select   => [qw/feature_id uniquename/],
        prefetch => 'dbxref'
    }
);

opendir( DIR, $data_dir ) or die $!;

$tempFile = File::Temp->new();
my $gff3_db = Bio::DB::SeqFeature::Store->new(
    -adaptor => 'DBI::SQLite',
    -dsn     => "dbi:SQLite:dbname=$tempFile",
    -create  => 1
);

my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(
    -store   => $gff3_db,
    -verbose => 1,
    -fast    => 1
);

while ( my $file = readdir(DIR) ) {
    $loader->load( $data_dir . $file );
}

my @genes = $gff3_db->get_features_by_type('gene');
for my $gene (@genes) {
    my $ddb_id     = $gene->seq_id;
    my @attributes = $gene->attributes;
    my $gene_id    = $attributes[1][0];

GENE:
    while ( my $row = $gene_rs->next ) {

        if ( $gene_id = $row->dbxref->accession ) {
            my $gene_name = $row->uniquename;
            my $gp_row    = $gp_schema->resultset('LocusGp')->search(
                { locus_no => $row->feature_id, },
                {   rows     => 1,
                    prefetch => 'locus_gene_product'
                }
            )->single;
            if ( !$gp_row ) {

              #print STDERR "NO gene product name for $gene_id\n" if $verbose;
                next;
            }

            my $gene_product = $gp_row->locus_gene_product->gene_product;
            if (   $gene_product eq 'unknown'
                or $gene_product eq 'pseudogene' )
            {
            #print STDERR "Skipping gene product $gene_product\n" if $verbose;
                next;
            }

            my $syn_rs
                = $syn_schema->resultset('Sequence::Synonym')
                ->search(
                { 'feature_synonyms.feature_id' => $row->feature_id, },
                { join                          => 'feature_synonyms' } );

            my $syn_name = "";
            if ( !$syn_rs ) {
                print STDERR "NO synonym for $gene_id\n";
                next;
            }
            else {
                while ( my $syn_row = $syn_rs->next ) {
                    $syn_name = $syn_name . $syn_row->name . ",";
                }
            }
            $syn_name =~ s/(,)+$//;
            $out_file->write(
                "$ddb_id\t$gene_id\t$gene_name\t$gene_product\t$syn_name\n");
            print STDOUT "$gene_id\t$gene_name\n";
        }
        else {
            next GENE;
        }
    }
}