--- - 2023-04-24 Initial repository creation, using ds_souschef.pl - 2023-05-05 adf: pulled ncRNA sequences out of mRNA fasta files, made mrna_primary isoforms consistent with protein/cds_primary isoforms - 2023-08-15 adf: fixed https://github.com/legumeinfo/datastore-issues/issues/175 with: zcat vicfa.Hedin2.gnm1.ann1.PTNK.gene_models_main.gff3.gz | ~/datastore-specifications/scripts/add_IDs_to_gff_features.pl --clobber_type CDS --clobber_type exon --clobber_type three_prime_UTR --clobber_type five_prime_UTR 2> feature_id_remapping.txt | bgzip -c -l9 > tmp.gz; mv tmp.gz vicfa.Hedin2.gnm1.ann1.PTNK.gene_models_main.gff3.gz; tabix -p gff -C vicfa.Hedin2.gnm1.ann1.PTNK.gene_models_main.gff3.gz - 2024-06-23 adf: addressed issues being caused in intermine code by ncRNA features by partitioning non-coding features into a separate file, basically: zcat vicfa.Hedin2.gnm1.ann1.PTNK.gene_models_main.gff3.gz | ~/datastore-specifications/scripts/partition_noncoding.pl > coding 2> noncoding note that some genes have both mRNA and ncRNA children and I put these into both files in the interest of making each one valid on its own