get_data.sh

mkdir -p valid_ids_data
echo 'systematic_id	primary_name	synonyms' > valid_ids_data/gene_IDs_names.tsv
curl -k https://www.pombase.org/data/names_and_identifiers/gene_IDs_names.tsv | tail -n+3 >> valid_ids_data/gene_IDs_names.tsv

# qualifier_changes from pre-svn downloaded from release
curl -L https://github.com/pombase/genome_changelog/releases/latest/download/pre_svn_qualifier_changes_file.tsv > gene_changes_comments_and_pmids/pre_svn_qualifier_changes_file.tsv

# get latest genome contig files
mkdir -p latest_genome

contigs='chromosome1 chromosome2 chromosome3 mating_type_region pMIT telomeric'
for contig in $contigs
do
    svn export --force https://curation.pombase.org/pombe-embl-repo/trunk/${contig}.contig latest_genome/${contig}.contig
done